Hello Cruzeiro,
Thanks a lot for your reply! It's helpful. I removed all the constant pH options in the min.in file and the minimization run well. But I still don't know why and wondering what will happen if I add constant pH options during heating or product MD run? Why? Do you have some cases of CpHMD in explicit solvent model?
Hoping for your reply. Thank you!
Best wishes,
Yao Li,
PhD candidate
School of life science,
Tsinghua University, China
> -----原始邮件-----
> 发件人: amber-request.ambermd.org
> 发送时间: 2018-05-30 03:00:01 (星期三)
> 收件人: amber.ambermd.org
> 抄送:
> 主题: AMBER Digest, Vol 2306, Issue 1
>
> Send AMBER mailing list submissions to
> amber.ambermd.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.ambermd.org/mailman/listinfo/amber
> or, via email, send a message with subject or body 'help' to
> amber-request.ambermd.org
>
> You can reach the person managing the list at
> amber-owner.ambermd.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: SHAKEH: Extra bond between hydrogen atoms of TIP3 water
> model (Sadegh Faramarzi Ganjabad)
> 2. AMBER NFE SMD calculation with new collective variable
> (georg.kuenze.vanderbilt.edu)
> 3. Re: ABMD with multiple walkers (Feng Pan)
> 4. AMBER: trouble while running constant pH simulation (??)
> 5. Re: ABMD with multiple walkers (Qinghua Liao)
> 6. Re: AMBER: trouble while running constant pH simulation (??)
> 7. Re: AMBER: trouble while running constant pH simulation
> (Cruzeiro,Vinicius Wilian D)
> 8. Re: AMBER TI more examples (David A Case)
> 9. Re: Reservoir REMD using GPUs (Hurst, Travis C (MU-Student))
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 28 May 2018 16:29:46 -0400
> From: Sadegh Faramarzi Ganjabad <safaramarziganjabad.mix.wvu.edu>
> Subject: Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3
> water model
> To: amber.ambermd.org
> Message-ID:
> <CAM8z6QV+BN9O9QaYWMH8vhT2vT5uPdU4aGiQi3BQBozN7Xc3dQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
>
> I think I found out why AMBER gave that error. The inputs from CHARMM
> should not have the extra bond between the two hydrogen atoms of water
> molecules. I regenerated my psf/pdb files using Automatic PSF Builder
> plugin on VMD, which does not add that extra bond. Then I converted those
> files to AMBER inputs, and it works fine.
>
> Thanks,
> Sadegh Faramarzi,
> Research Assistant
> West Virginia University, Department of Chemistry
> Email:safaramarziganjabad.mix.wvu.edu
>
> On Wed, May 23, 2018 at 3:36 PM, Sadegh Faramarzi Ganjabad <
> safaramarziganjabad.mix.wvu.edu> wrote:
>
> > David,
> >
> > I'm not using top_all27_na.rtf or top_all27_prot_na.rtf. Here is the
> > syntax I use on parmed
> >
> >
> > chamber -top top_all36_lipid.rtf -param par_all36_lipid.prm -param
> > par_all36m_prot.prm -param par_all36_cgenff.prm -param par_all36_na.prm
> > -param ddm2.prm -param par_all36_carb.prm -param par_all36_prot_mod.prm
> > -str toppar_all36_lipid_detergent.str -str ../retinal-depro.str -toppar
> > toppar_water_ions_fixed.str -psf all-ion.psf -crd all-ion_new.pdb -nocmap
> > -box 75.4,75.13,83.8
> >
> > I checked the files above, they don't have the error that top_all27_na.rtf
> > has. Interestingly. I have tested the same param/topology files for another
> > system for which the water molecules are generated with VMD. They work
> > well. But for the system generated with CHARM-GUI website I get that SHAKEH
> > error for water molecules.
> >
> > I'm using AmberTools 18. I'm sending you all the files I use. I looked at
> > the pdb file, atoms with indices 23639, 23638, 23640 are the first water
> > molecule that appears on pdb file after the bilayer atoms.
> >
> >
> >
> > Date: Tue, 22 May 2018 15:53:54 -0400
> > From: David A Case <david.case.rutgers.edu>
> > Subject: Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3
> > water model
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <20180522195354.5nge63p6hrxxgdk2.vpn-client-172-16-8-12.
> > rutgers.edu>
> > Content-Type: text/plain; charset=us-ascii
> >
> > > On Mon, May 21, 2018, Sadegh Faramarzi Ganjabad wrote:
> > > >
> > > > I have converted CHARMM inputs to AMBER inputs. Not sure why but there
> > are
> > > > extra bonds between two hydrogen atoms in the water molecules in the
> > > > original CHARMM files. When I try to run the AMBER inputs it complains
> > > > about those extra bonds. Here is the error I get
> > > >
> > > > Hydrogen atom 23639 appears to have multiple bonds to atoms 23638 and
> > > > 23640 which is illegal for SHAKEH.
> > Please see the recent mailing list entry about a similar problem. Are
> > you using top_all27_na.rtf or top_all27_prot_na.rtf? If, so that post
> > might
> > have help for you.
> >
> > If the hydrogens above are really in water, can you say exactly how you
> > convert CHARMM to AMBER inputs? Which version of AmberTools do you
> > have?
> >
> > ...thx...dac
> >
> > Thanks,
> > Sadegh Faramarzi,
> > Research Assistant
> > West Virginia University, Department of Chemistry
> > Email:safaramarziganjabad.mix.wvu.edu
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 28 May 2018 16:51:41 -0400
> From: <georg.kuenze.vanderbilt.edu>
> Subject: [AMBER] AMBER NFE SMD calculation with new collective
> variable
> To: <amber.ambermd.org>
> Message-ID: <006e01d3f6c5$aebc42c0$0c34c840$.vanderbilt.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello Amber community,
>
> I am using Amber's NFE module for doing some steered MD. I have implemented
> a new collective variable that represents the binding between two residues
> of a salt bridge and the translation of one of them relative to a third
> residue. The code compiles without errors and a SMD simulation starts as
> expected. However, after a few ten thousand steps the vlimit is exceeded. I
> suppose this error is because of the new collective variable because
> simulations with other collective variables work fine. I am trying to find
> out what is the most likely reason for this error. Can it be related to how
> the gradient is calculated? Maybe it gets too steep? Any help would be
> appreciated.
>
>
>
> Thanks!
>
> Georg
>
>
>
> Here are the last lines from the mdout file:
>
>
>
> NSTEP = 71000 TIME(PS) = 205242.000 TEMP(K) = 309.94 PRESS =
> 0.0
>
> Etot = -112213.8769 EKtot = 53399.5438 EPtot =
> -165613.4207
>
> BOND = 4686.9923 ANGLE = 18941.9690 DIHED =
> 12435.7397
>
> 1-4 NB = 4282.1305 1-4 EEL = -699.7597 VDWAALS =
> 5129.6937
>
> EELEC = -210390.1862 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> Ewald error estimate: 0.7925E-04
>
> ----------------------------------------------------------------------------
> --
>
>
>
> vlimit exceeded for step 71432; vmax = 20.3955
>
> vlimit exceeded for step 71433; vmax = 99.6675
>
>
>
> Coordinate resetting (SHAKE) cannot be accomplished,
>
> deviation is too large
>
> NITER, NIT, LL, I and J are : 0 0 1095 2149 2150
>
>
>
> Note: This is usually a symptom of some deeper
>
> problem with the energetics of the system.
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 28 May 2018 21:01:21 -0400
> From: Feng Pan <fpan3.ncsu.edu>
> Subject: Re: [AMBER] ABMD with multiple walkers
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAHZ=aZeB3J1ABCM_RLs=2LDpzorYORbP_xRXZWrbFRkVmqzLvQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Leading to 0 walker means this replica will be removed, replaced by another
> replica which leads to 2 walkers.
>
> Leading to 1 walker means the walker will stay with itself, but the index
> may
> shift to the next one when it has neighboring replica leading to 0 walkers.
>
> When it is converged, each replica should lead to 1 walker, which means
> the selection actually does not take effects.
>
> Feng
>
>
> On Mon, May 28, 2018 at 8:36 AM, Qinghua Liao <scorpio.liao.gmail.com>
> wrote:
>
> > Hello Feng,
> >
> > Thanks a lot for your reply.
> >
> > A few more questions:
> >
> > Leading to 0 walker means that the walker will be stayed with itself or
> > copied by another walker
> > which leads to 2 walkers?
> > Leading to 1 walker means that this walker might be stayed with itself or
> > can copied by another walker which leads to 1 walker too?
> >
> > What would be the selection scores of all walkers if the ABMD with
> > multiple walkers is converged?
> >
> > Thanks so much!
> >
> >
> > All the best,
> > Qinghua
> >
> >
> >
> > On 05/28/2018 04:05 AM, Feng Pan wrote:
> > > Hi, Qinghua
> > >
> > > Yes, you are right, I made a mistake. I check the codes. A random number
> > > between 0 to 1/8
> > > should be added to the score.
> > > For example, for the first replica, if the sum is below 1/8 (like the
> > score
> > > is below 1/8 and
> > > the random number is also small), this replica leads to zero walkers. If
> > > the sum is between
> > > 1/8 and 2/8, leads to 1 walker. The following replicas will be calculated
> > > to make sure the
> > > total number of walkers is 8.
> > > So basically when you see the score is below 1/8, the walker could be 0
> > or
> > > 1.
> > >
> > >
> > > When I say walkers will be copied, I mean the coordinates
> > > will be copied.
> > >
> > > Best
> > > Feng
> > >
> > > On Sun, May 27, 2018 at 5:08 PM, Qinghua Liao <scorpio.liao.gmail.com>
> > > wrote:
> > >
> > >> Dear Feng,
> > >>
> > >> Thanks a lot for your explanation.
> > >>
> > >> Following your explanation, I also found that there are some walkers
> > >> which have the scores
> > >> between 1/8 and 2/8, but the walkers were not copied to 2 walkers.
> > >>
> > >> When the score is less than 1/8, the walker will be kept itself, then
> > >> the sign is "=> 0" or "=> 1"
> > >>
> > >> About the term "walkers will be copied", are coordinates copied or
> > >> selection score (weight)? Thanks a lot!
> > >>
> > >>
> > >> All the best,
> > >> Qinghua
> > >>
> > >> On 05/27/2018 04:16 AM, Feng Pan wrote:
> > >>> Hi, Qinghua
> > >>>
> > >>> the selection score is the ratio of the replica selection weight over
> > the
> > >>> total weight,
> > >>> so if you have 8 replicas here, and the score is below 1/8, the walker
> > >> will
> > >>> keep
> > >>> itself. If the score is between 1/8 and 2/8, the walker will be copied
> > >> to 2
> > >>> walkers, as
> > >>> shown like => 2 walkers.
> > >>>
> > >>> When the entropy is above the threshold, the selection will be
> > >> calculated,
> > >>> but if
> > >>> every selection score is below 1/8, there will be no resampling, every
> > >>> walker will
> > >>> be kept just itself.
> > >>>
> > >>> Best
> > >>> Feng
> > >>>
> > >>> On Fri, May 25, 2018 at 7:00 PM, Qinghua Liao <scorpio.liao.gmail.com>
> > >>> wrote:
> > >>>
> > >>>> Hello Amber developers,
> > >>>>
> > >>>> Currently, I am running ABMD with multiple walkers, but I have some
> > >>>> questions regarding interpreting the output.
> > >>>> Here is my input for the multiple walkers:
> > >>>>
> > >>>> selection_freq = 500
> > >>>> selection_constant = 0.00001
> > >>>> selection_epsilon = 0.0
> > >>>>
> > >>>> And here are some output from the simulations:
> > >>>> #
> > >>>> NFE : selection score for walker 1 is 0.930991 / 7.992304 = 0.116
> > =>
> > >> 0
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 2 is 0.881570 / 7.992304 = 0.110
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 3 is 0.945704 / 7.992304 = 0.118
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 4 is 0.951837 / 7.992304 = 0.119
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 5 is 0.973335 / 7.992304 = 0.122
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 6 is 1.103148 / 7.992304 = 0.138
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 7 is 0.967854 / 7.992304 = 0.121
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 8 is 1.237866 / 7.992304 = 0.155
> > =>
> > >> 2
> > >>>> walker(s)
> > >>>> NFE : Selection entropy 0.005597 is greater than threshold
> > 0.000000
> > >>>> NFE : Selection resampling : new 1 comes from 2
> > >>>> #
> > >>>> #
> > >>>> NFE : selection score for walker 1 is 1.042757 / 7.817606 = 0.133
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 2 is 0.956335 / 7.817606 = 0.122
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 3 is 0.775833 / 7.817606 = 0.099
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 4 is 0.906343 / 7.817606 = 0.116
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 5 is 0.938005 / 7.817606 = 0.120
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 6 is 0.851424 / 7.817606 = 0.109
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 7 is 1.232238 / 7.817606 = 0.158
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : selection score for walker 8 is 1.114672 / 7.817606 = 0.143
> > =>
> > >> 1
> > >>>> walker(s)
> > >>>> NFE : Selection entropy 0.009795 is greater than threshold
> > 0.000000
> > >>>> #
> > >>>>
> > >>>> How should I understand the selection score, how is it calculated?
> > What
> > >>>> does "=>0 (1,2) walker(s)" mean?
> > >>>> For the first assessment, the selection entropy is 0.005597,
> > >>>> which is greater than the threshold 0.0, and then there is a selection
> > >>>> resampling (new 1 comes from 2). For the second
> > >>>> assessment, the selection entropy is also greater than the threshold,
> > >>>> but there is no resampling. Why is this different?
> > >>>>
> > >>>> I appreciate any of your responds.
> > >>>>
> > >>>>
> > >>>> All the best,
> > >>>> Qinghua
> > >>>>
> > >>>> _______________________________________________
> > >>>> AMBER mailing list
> > >>>> AMBER.ambermd.org
> > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>
> > >>>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Feng Pan
> Ph.D.
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 29 May 2018 10:35:06 +0800 (GMT+08:00)
> From: ?? <liyao17.mails.tsinghua.edu.cn>
> Subject: [AMBER] AMBER: trouble while running constant pH simulation
> To: amber <amber.ambermd.org>
> Message-ID:
> <7cc6d463.6098.163a9bfc32a.Coremail.liyao17.mails.tsinghua.edu.cn>
> Content-Type: text/plain; charset=UTF-8
>
> Hi all,
>
>
> I'm trying to run constant pH simulation in explicit solvent model with Amber16(AmberTools17). I generated a cpin file according to the tutorial and type command:
> sander -O -i 01_min.in -o 01_min.out -p radii_prmtop -c inpcrd -r 01_min.rst -inf 01_min.mdinfo -cpin cpin
>
>
> to run minimization. It came out like this:
> At line 174 of file constantph.F90 (unit = 18, file = 'cpin')
> Fortran runtime error: Cannot match namelist object name 'residue:
>
>
> And this is a part of my cpin file:
> &CNSTPH
> CHRGDAT=-0.3479,0.2747,-0.1354,0.1212,-0.0414,0.081,0.081,-0.0012,-0.1513,
> 0.3866,-0.017,0.2681,-0.1718,0.3911,-0.1141,0.2317,0.7341,-0.5894,-0.3479,
> 0.2747,-0.1354,0.1212,-0.111,0.0402,0.0402,-0.0266,-0.3811,0.3649,0.2057,
> 0.1392,-0.5727,0.0,0.1292,0.1147,0.7341,-0.5894,-0.3479,0.2747,-0.1354,0.1212,
> -0.1012,0.0367,0.0367,0.1868,-0.5432,0.0,0.1635,0.1435,-0.2795,0.3339,-0.2207,
> PROTCNT=2,1,1,0,1,1,1,1,0,1,1,1,1,
> RESNAME='System: Unknown','Residue: HIP 33','Residue: AS4 38',
> 'Residue: GL4 39','Residue: GL4 57','Residue: AS4 67','Residue: HIP 70',
> 'Residue: GL4 73','Residue: GL4 83','Residue: AS4 86','Residue: AS4 91',
> 'Residue: GL4 92','Residue: GL4 96','Residue: AS4 100','Residue: GL4 116',
>
>
> Is that a problem about my fortran compiler or about the file? I have no idea. Can you have a look on this? Many many thanks!
>
>
>
>
> Yours sincerely,
> Yao Li
>
> ------------------------------
>
> Message: 5
> Date: Tue, 29 May 2018 09:31:31 +0200
> From: Qinghua Liao <scorpio.liao.gmail.com>
> Subject: Re: [AMBER] ABMD with multiple walkers
> To: amber.ambermd.org
> Message-ID: <39d66488-2ad9-1c33-c42e-4771b5d44771.gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hello Feng,
>
> Thanks a lot for your clarification. I understand it now!
>
>
> All the best,
> Qinghua
>
> On 05/29/2018 03:01 AM, Feng Pan wrote:
> > Leading to 0 walker means this replica will be removed, replaced by another
> > replica which leads to 2 walkers.
> >
> > Leading to 1 walker means the walker will stay with itself, but the index
> > may
> > shift to the next one when it has neighboring replica leading to 0 walkers.
> >
> > When it is converged, each replica should lead to 1 walker, which means
> > the selection actually does not take effects.
> >
> > Feng
> >
> >
> > On Mon, May 28, 2018 at 8:36 AM, Qinghua Liao <scorpio.liao.gmail.com>
> > wrote:
> >
> >> Hello Feng,
> >>
> >> Thanks a lot for your reply.
> >>
> >> A few more questions:
> >>
> >> Leading to 0 walker means that the walker will be stayed with itself or
> >> copied by another walker
> >> which leads to 2 walkers?
> >> Leading to 1 walker means that this walker might be stayed with itself or
> >> can copied by another walker which leads to 1 walker too?
> >>
> >> What would be the selection scores of all walkers if the ABMD with
> >> multiple walkers is converged?
> >>
> >> Thanks so much!
> >>
> >>
> >> All the best,
> >> Qinghua
> >>
> >>
> >>
> >> On 05/28/2018 04:05 AM, Feng Pan wrote:
> >>> Hi, Qinghua
> >>>
> >>> Yes, you are right, I made a mistake. I check the codes. A random number
> >>> between 0 to 1/8
> >>> should be added to the score.
> >>> For example, for the first replica, if the sum is below 1/8 (like the
> >> score
> >>> is below 1/8 and
> >>> the random number is also small), this replica leads to zero walkers. If
> >>> the sum is between
> >>> 1/8 and 2/8, leads to 1 walker. The following replicas will be calculated
> >>> to make sure the
> >>> total number of walkers is 8.
> >>> So basically when you see the score is below 1/8, the walker could be 0
> >> or
> >>> 1.
> >>>
> >>>
> >>> When I say walkers will be copied, I mean the coordinates
> >>> will be copied.
> >>>
> >>> Best
> >>> Feng
> >>>
> >>> On Sun, May 27, 2018 at 5:08 PM, Qinghua Liao <scorpio.liao.gmail.com>
> >>> wrote:
> >>>
> >>>> Dear Feng,
> >>>>
> >>>> Thanks a lot for your explanation.
> >>>>
> >>>> Following your explanation, I also found that there are some walkers
> >>>> which have the scores
> >>>> between 1/8 and 2/8, but the walkers were not copied to 2 walkers.
> >>>>
> >>>> When the score is less than 1/8, the walker will be kept itself, then
> >>>> the sign is "=> 0" or "=> 1"
> >>>>
> >>>> About the term "walkers will be copied", are coordinates copied or
> >>>> selection score (weight)? Thanks a lot!
> >>>>
> >>>>
> >>>> All the best,
> >>>> Qinghua
> >>>>
> >>>> On 05/27/2018 04:16 AM, Feng Pan wrote:
> >>>>> Hi, Qinghua
> >>>>>
> >>>>> the selection score is the ratio of the replica selection weight over
> >> the
> >>>>> total weight,
> >>>>> so if you have 8 replicas here, and the score is below 1/8, the walker
> >>>> will
> >>>>> keep
> >>>>> itself. If the score is between 1/8 and 2/8, the walker will be copied
> >>>> to 2
> >>>>> walkers, as
> >>>>> shown like => 2 walkers.
> >>>>>
> >>>>> When the entropy is above the threshold, the selection will be
> >>>> calculated,
> >>>>> but if
> >>>>> every selection score is below 1/8, there will be no resampling, every
> >>>>> walker will
> >>>>> be kept just itself.
> >>>>>
> >>>>> Best
> >>>>> Feng
> >>>>>
> >>>>> On Fri, May 25, 2018 at 7:00 PM, Qinghua Liao <scorpio.liao.gmail.com>
> >>>>> wrote:
> >>>>>
> >>>>>> Hello Amber developers,
> >>>>>>
> >>>>>> Currently, I am running ABMD with multiple walkers, but I have some
> >>>>>> questions regarding interpreting the output.
> >>>>>> Here is my input for the multiple walkers:
> >>>>>>
> >>>>>> selection_freq = 500
> >>>>>> selection_constant = 0.00001
> >>>>>> selection_epsilon = 0.0
> >>>>>>
> >>>>>> And here are some output from the simulations:
> >>>>>> #
> >>>>>> NFE : selection score for walker 1 is 0.930991 / 7.992304 = 0.116
> >> =>
> >>>> 0
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 2 is 0.881570 / 7.992304 = 0.110
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 3 is 0.945704 / 7.992304 = 0.118
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 4 is 0.951837 / 7.992304 = 0.119
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 5 is 0.973335 / 7.992304 = 0.122
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 6 is 1.103148 / 7.992304 = 0.138
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 7 is 0.967854 / 7.992304 = 0.121
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 8 is 1.237866 / 7.992304 = 0.155
> >> =>
> >>>> 2
> >>>>>> walker(s)
> >>>>>> NFE : Selection entropy 0.005597 is greater than threshold
> >> 0.000000
> >>>>>> NFE : Selection resampling : new 1 comes from 2
> >>>>>> #
> >>>>>> #
> >>>>>> NFE : selection score for walker 1 is 1.042757 / 7.817606 = 0.133
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 2 is 0.956335 / 7.817606 = 0.122
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 3 is 0.775833 / 7.817606 = 0.099
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 4 is 0.906343 / 7.817606 = 0.116
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 5 is 0.938005 / 7.817606 = 0.120
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 6 is 0.851424 / 7.817606 = 0.109
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 7 is 1.232238 / 7.817606 = 0.158
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : selection score for walker 8 is 1.114672 / 7.817606 = 0.143
> >> =>
> >>>> 1
> >>>>>> walker(s)
> >>>>>> NFE : Selection entropy 0.009795 is greater than threshold
> >> 0.000000
> >>>>>> #
> >>>>>>
> >>>>>> How should I understand the selection score, how is it calculated?
> >> What
> >>>>>> does "=>0 (1,2) walker(s)" mean?
> >>>>>> For the first assessment, the selection entropy is 0.005597,
> >>>>>> which is greater than the threshold 0.0, and then there is a selection
> >>>>>> resampling (new 1 comes from 2). For the second
> >>>>>> assessment, the selection entropy is also greater than the threshold,
> >>>>>> but there is no resampling. Why is this different?
> >>>>>>
> >>>>>> I appreciate any of your responds.
> >>>>>>
> >>>>>>
> >>>>>> All the best,
> >>>>>> Qinghua
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 29 May 2018 15:54:18 +0800 (GMT+08:00)
> From: ?? <liyao17.mails.tsinghua.edu.cn>
> Subject: Re: [AMBER] AMBER: trouble while running constant pH
> simulation
> To: amber <amber.ambermd.org>
> Message-ID:
> <35ea014f.65f7.163aae3ffaf.Coremail.liyao17.mails.tsinghua.edu.cn>
> Content-Type: text/plain; charset=UTF-8
>
> My command to generate new topology file and cpin file is:
>
>
> cpinutil.py -resnames GL4 AS4 -p prmtop \-op new_radii_prmtop -resnames HIP GL4 AS4 -igb 2 -o cpin
>
>
> -----????-----
> ???:"??" <liyao17.mails.tsinghua.edu.cn>
> ????:2018-05-29 10:35:06 (???)
> ???: amber <amber.ambermd.org>
> ??:
> ??: AMBER: trouble while running constant pH simulation
>
>
> Hi all,
>
>
> I'm trying to run constant pH simulation in explicit solvent model with Amber16(AmberTools17). I generated a cpin file according to the tutorial and type command:
> sander -O -i 01_min.in -o 01_min.out -p radii_prmtop -c inpcrd -r 01_min.rst -inf 01_min.mdinfo -cpin cpin
>
>
> to run minimization. It came out like this:
> At line 174 of file constantph.F90 (unit = 18, file = 'cpin')
> Fortran runtime error: Cannot match namelist object name 'residue:
>
>
> And this is a part of my cpin file:
> &CNSTPH
> CHRGDAT=-0.3479,0.2747,-0.1354,0.1212,-0.0414,0.081,0.081,-0.0012,-0.1513,
> 0.3866,-0.017,0.2681,-0.1718,0.3911,-0.1141,0.2317,0.7341,-0.5894,-0.3479,
> 0.2747,-0.1354,0.1212,-0.111,0.0402,0.0402,-0.0266,-0.3811,0.3649,0.2057,
> 0.1392,-0.5727,0.0,0.1292,0.1147,0.7341,-0.5894,-0.3479,0.2747,-0.1354,0.1212,
> -0.1012,0.0367,0.0367,0.1868,-0.5432,0.0,0.1635,0.1435,-0.2795,0.3339,-0.2207,
> PROTCNT=2,1,1,0,1,1,1,1,0,1,1,1,1,
> RESNAME='System: Unknown','Residue: HIP 33','Residue: AS4 38',
> 'Residue: GL4 39','Residue: GL4 57','Residue: AS4 67','Residue: HIP 70',
> 'Residue: GL4 73','Residue: GL4 83','Residue: AS4 86','Residue: AS4 91',
> 'Residue: GL4 92','Residue: GL4 96','Residue: AS4 100','Residue: GL4 116',
>
>
> Is that a problem about my fortran compiler or about the file? I have no idea. Can you have a look on this? Many many thanks!
>
>
>
>
> Yours sincerely,
> Yao Li
>
> ------------------------------
>
> Message: 7
> Date: Tue, 29 May 2018 12:58:06 +0000
> From: "Cruzeiro,Vinicius Wilian D" <vwcruzeiro.ufl.edu>
> Subject: Re: [AMBER] AMBER: trouble while running constant pH
> simulation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <8E83E1F9-CC3A-4434-A59F-FA597206C5B2.ufl.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Yao,
>
> In explicit solvent, the prmtop file you point as an output in the flag -op in the cpinutil.py command is the one you need to use in the sander command. According to the commands you sent, it seems you are using a different file in your sander command.
>
> Also, check your 01_min.in file to make sure you are not activating the constant pH option during the minimization run.
>
> I hope this helps,
> Best,
>
>
> Vin?cius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633<tel:+1(352)846-1633>
>
> On May 29, 2018, at 3:55 AM, ?? <liyao17.mails.tsinghua.edu.cn<mailto:liyao17.mails.tsinghua.edu.cn>> wrote:
>
> My command to generate new topology file and cpin file is:
>
>
> cpinutil.py -resnames GL4 AS4 -p prmtop \-op new_radii_prmtop -resnames HIP GL4 AS4 -igb 2 -o cpin
>
>
> -----????-----
> ???:"??" <liyao17.mails.tsinghua.edu.cn<mailto:liyao17.mails.tsinghua.edu.cn>>
> ????:2018-05-29 10:35:06 (???)
> ???: amber <amber.ambermd.org<mailto:amber.ambermd.org>>
> ??:
> ??: AMBER: trouble while running constant pH simulation
>
>
> Hi all,
>
>
> I'm trying to run constant pH simulation in explicit solvent model with Amber16(AmberTools17). I generated a cpin file according to the tutorial and type command:
> sander -O -i 01_min.in -o 01_min.out -p radii_prmtop -c inpcrd -r 01_min.rst -inf 01_min.mdinfo -cpin cpin
>
>
> to run minimization. It came out like this:
> At line 174 of file constantph.F90 (unit = 18, file = 'cpin')
> Fortran runtime error: Cannot match namelist object name 'residue:
>
>
> And this is a part of my cpin file:
> &CNSTPH
> CHRGDAT=-0.3479,0.2747,-0.1354,0.1212,-0.0414,0.081,0.081,-0.0012,-0.1513,
> 0.3866,-0.017,0.2681,-0.1718,0.3911,-0.1141,0.2317,0.7341,-0.5894,-0.3479,
> 0.2747,-0.1354,0.1212,-0.111,0.0402,0.0402,-0.0266,-0.3811,0.3649,0.2057,
> 0.1392,-0.5727,0.0,0.1292,0.1147,0.7341,-0.5894,-0.3479,0.2747,-0.1354,0.1212,
> -0.1012,0.0367,0.0367,0.1868,-0.5432,0.0,0.1635,0.1435,-0.2795,0.3339,-0.2207,
> PROTCNT=2,1,1,0,1,1,1,1,0,1,1,1,1,
> RESNAME='System: Unknown','Residue: HIP 33','Residue: AS4 38',
> 'Residue: GL4 39','Residue: GL4 57','Residue: AS4 67','Residue: HIP 70',
> 'Residue: GL4 73','Residue: GL4 83','Residue: AS4 86','Residue: AS4 91',
> 'Residue: GL4 92','Residue: GL4 96','Residue: AS4 100','Residue: GL4 116',
>
>
> Is that a problem about my fortran compiler or about the file? I have no idea. Can you have a look on this? Many many thanks!
>
>
>
>
> Yours sincerely,
> Yao Li
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-DrdQBJXyFyocKAWXc&m=Xmuu-upi2iJ89oUO-g3fYiLVG7TPFawnMcOO3b5_3j0&s=HB77r1QPzDuaREXZg1jBgG_mbl8oPgQTuZvmB-9pMFk&e=
>
> ------------------------------
>
> Message: 8
> Date: Tue, 29 May 2018 09:24:41 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] AMBER TI more examples
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20180529132441.gsapotasnydwmpsf.vpn-client-172-16-8-12.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Thu, May 24, 2018, Omoto, Kiyoyuki wrote:
> >
> > I am learning AMBER TI, but unfortunately it seems that there's only a
> > couple of tutorials in Web.
> >
> > Do you have a tutorial for a more drug-like molecules complexed with a
> > protein.
>
> Just to be sure: did you look at this one:
>
> http://ambermd.org/tutorials/advanced/tutorial9/index.html
>
> It covers small molecules binding to T4-lysozyme. It's true that the
> molecules there are not all that "drug-like", but it still seems like a
> pretty relevant tutorial, especially if you are having problems creating
> input files and command-line scripts.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Tue, 29 May 2018 15:09:01 +0000
> From: "Hurst, Travis C (MU-Student)" <tchvw5.mail.missouri.edu>
> Subject: Re: [AMBER] Reservoir REMD using GPUs
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <DM5PR0101MB311636B9DB0C0FB6B54E8816C96D0.DM5PR0101MB3116.prod.exchangelabs.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Professor Simmerling,
>
>
> Thank you for your help!
>
>
> After using the createreservoir option to build the reservoir, I was not sure what flag to use to load the NetCDF reservoir into memory when beginning the R-REMD simulation using sander. After digging through the code, I found the reservoir_ncid value should be changed from -1 to read in the NetCDF reservoir, but I did not get much farther on that. Once I realized that the GPUs are not supported yet, I started working to use some of the other methods.
>
>
> That is great that pmemd support is coming soon for R-REMD! Will the hybrid solvent model be supported soon as well?
>
>
> Best,
>
>
> Travis
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, May 25, 2018 12:07:02 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Reservoir REMD using GPUs
>
> sorry for the delay in replying. In the current release, R-REMD is only
> supported in sander. We plan to release pmemd support this year as a patch
> to Amber 18. Dan Roe might be able to better answer your questions about
> using the createreservoir command in cpptraj - is this a problem you're
> having with sander, or in the cpptraj part?
>
> The only recent enhanced sampling I have seen for RNA in explicit solvent
> is work from Christina Bergonzo with Tom Cheatham, and the systems are much
> smaller than 20nt. I think that RNA of that size in explicit solvent will
> still be very challenging.
> CS
>
> On Wed, May 16, 2018 at 6:25 PM, Hurst, Travis C (MU-Student) <
> tchvw5.mail.missouri.edu> wrote:
>
> > Hello Everyone,
> >
> >
> > I have been doing some REMD simulations on a small (20 nt) RNA hairpin in
> > explicit solvent using Amber16, which have been going great thanks to the
> > manual and help from the archive. I am using the results from these runs to
> > build PMFs for the hairpin.
> >
> >
> > Now, I am interested in using a high temperature structure reservoir to
> > speed up the convergence of the simulations. However, when I try to use
> > pmemd.cuda.MPI to run the simulations, pmemd does not recognize the -rremd
> > flag. Is there a way to use GPUs for running R-REMD simulations or is
> > sander.MPI the only option? I have gotten the R-REMD simulation to work
> > using sander.MPI, but mdinfo estimated about 5700 hours to finish, so
> > incorporating the GPUs is definitely necessary for production runs if I use
> > this method.
> >
> >
> > Additionally, I found the createreservoir command in the manual and built
> > a structure reservoir using that, but I am not sure how to load this into
> > memory for the R-REMD simulations to properly read the files. I tried
> > placing the name of the reservoir after the -reservoir flag, but the
> > simulation cannot find the files. Before finding the createreservoir
> > command, I built a reservoir by opening cpptraj, reading in the
> > parm/trajectory files, and using trajout ./reserv/frame restart to build
> > the reservoir. Then, I changed the file numbers from the command line to
> > fit the format from the manual. This seems to work ok, but the
> > createreservoir command works faster and uses much less memory.
> >
> >
> > Finally, if anyone has any advice on other enhanced sampling methods that
> > may be more appropriate for rapidly getting accurate PMFs for this system,
> > I am all ears.
> >
> >
> > Best,
> >
> >
> > Travis
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 2306, Issue 1
> **************************************
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 30 2018 - 09:00:03 PDT
