Re: [AMBER] AMBER Digest, Vol 1311, Issue 1

From: Robin Jain <robinjain.chem.gmail.com>
Date: Sat, 15 Aug 2015 14:28:47 +0530

Dear all,
I have used following MEOH parameters, Will you please check this and find
the problem.
Also i want to state that first i minimize my system , the heat and then
equilibration and production run.will u required input file also to know
about my problem.
Please solve my problem. Thanking You.

On Sat, Aug 15, 2015 at 12:30 AM, <amber-request.ambermd.org> wrote:

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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. ImportError: No module named mcpb.gene_model_files
> (Marcelo Andrade Chagas)
> 2. Job submission script for SGE (Himansu)
> 3. The protein is Leaving the water box! (Amber mail)
> 4. help in rdf (Robin Jain)
> 5. Re: The protein is Leaving the water box! (Jason Swails)
> 6. Re: Job submission script for SGE (Jason Swails)
> 7. Re: Job submission script for SGE (Gerald Monard)
> 8. Re: The protein is Leaving the water box! (Amber mail)
> 9. Re: The protein is Leaving the water box! (Jason Swails)
> 10. Re: help in rdf (Daniel Roe)
> 11. the better box size (Investigador Qu?mica)
> 12. Re: the better box size (Jason Swails)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 13 Aug 2015 16:14:22 -0300
> From: Marcelo Andrade Chagas <andrade.mchagas.gmail.com>
> Subject: [AMBER] ImportError: No module named mcpb.gene_model_files
> To: amber.ambermd.org
> Message-ID:
> <
> CAFAJS9zNPDJrFdUq2JFezxGswYLZcQr+UFhg1eHGwB6N6c+reQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear,
>
> the updated version of Ambertools14 for 15 lowering of the site and the
> Ambertools15
> Amber reinstalling the program because the "./update_amber --upgrade" has
> not worked.
>
> the network installation was concliuda and when I tried to call the routine
> MCPB.py the following message appears:
>
>
> [lqcmm.gibbs AmberTools]$ MCPB.py -h
>
> Traceback (most recent call last):
> File "/home/lqcmm/AMBER/amber14/bin/MCPB.py", line 46, in <module>
> from mcpb.gene_model_files import get_ms_resnames, gene_model_files
> ImportError: No module named mcpb.gene_model_files
>
>
> I'm using centOS.
>
> What could have been done wrong in install mode?
>
> Best regards
>
> Marcelo A.Chagas
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laborat?rio de Qu?mica Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Qu?mica da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 14 Aug 2015 05:20:59 +0530
> From: Himansu <himansubiswal.gmail.com>
> Subject: [AMBER] Job submission script for SGE
> To: amber.ambermd.org, david.case.rutgers.edu
> Message-ID:
> <
> CADWMTfiTYZELvaT78k3298uF4hNu4Jujpn17fV0maqh+nfEVwg.mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Amber users,
> Recently we installed AMBER14 and AMBER TOOLS 15 in our SGE HPC. We are
> using Tutorials to verify the installation. Currently we are using
> Tutorial: A room-temperature ionic liquid. The serial one is working but
> not the parallel one. I am attaching the job submission script (AMBER.sh)
> that I used for the parallel run for other software such as TURBOMOLE.
> Seeking your suggestions in this regard.
>
> Best regards,
> Himansu
> --
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> *Dr. Himansu S. Biswal*
> Assistant Professor
> School of Chemical Sciences,
> National Institute of Science
> Education and Research(NISER),
> Bhubaneswar-751005, Orissa, INDIA.
> Mob: +91 917 831 1188
>
> *E-mail :himansu.niser.ac.in <himansu.niser.ac.in>
> himansubiswal.gmail.com <himansubiswal.gmail.com>*
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 3
> Date: Fri, 14 Aug 2015 02:36:59 +0200
> From: Amber mail <amber.auc14.gmail.com>
> Subject: [AMBER] The protein is Leaving the water box!
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAJAn0fgjwXxmWLb7Fkq37UgWkMW3X-VGVhpZodajHx84abz54w.mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear AMBER users,
>
> I am performing a MD simulation using AMBER12 under the ff99SB force filed.
> Initially, the structure was neutralized and then solvated using TIP3P
> water model.
>
> After the minimization stage, a 50ps of MD simulation was performed from 0K
> to 100K. The system is then heated up in increments of 25K with 50ps of MD
> simulation at each temperature increment until the desired temperature of
> 310K was established.
>
> This the control file for heating (0-100)K
>
> Heat
> > &cntrl
> > imin=0,
> > ntx=1,
> > irest=0,
> > nstlim=25000,
> > dt=0.002,
> > ntf=2,
> > ntc=2,
> > tempi=0.0,
> > temp0=100.0,
> > ntpr=100,
> > ntwx=100,
> > cut=8.0,
> > ntb=2,
> > ntp=1,
> > ntt=3,
> > gamma_ln=1.0,
> > tautp=1.0,
> > taup=1.0,
> > pres0=1.01325,
> > nmropt=0,
> > ig=-1,
> > iwrap=1,
> > /
> >
>
> A 50 ns of MD simulation is going to be performed at 310K. Till now, I have
> got 20 ns out of 50 ns. This is the control file for the production step
>
> Production
> > &cntrl
> > imin=0,
> > ntx=5,
> > irest=1,
> > nstlim=5000000,
> > dt=0.002,
> > ntf=2,
> > ntc=2,
> > temp0=310.0,
> > tempi=310.0,
> > ntpr=5000,
> > ntwx=5000,
> > cut=8.0,
> > ntb=2,
> > ntp=1,
> > ntt=3,
> > gamma_ln=1.0,
> > ig=-1,
>
> nmropt=0,
> > iwrap=1,
> > /
> >
>
> The problem is that a part of the protein is leaving the water box after 20
> ns of the MD production
>
>
> ?
> Please correct me If I am wrong, since I used the wrapping option
> (iwrap=1), the water molecules should wrap (surround) any residue in case
> if it is trying to leave the water box. does this mean that these outer
> residues are being simulated now in vacuum?! If I am right, is setting
> ntb=2 (boundary conditions) works for this behavior, and there is no
> problem ?!
>
>
> Another question regarding the heating stage, below is the plot of
> Temperature vs. Time before production, I am wondering why the increase in
> the Temperature was not going smoothly and the equilibration did not reach
> at the end of the heating stage (like the results of the tutorials, which I
> performed before)
>
>
> ?A same pattern (sudden change) was also obtained for the Potential energy,
> Kinetic Energy and the Total Energy (in the heating stage)
>
> Thanks in advance!
> -------------- next part --------------
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> ------------------------------
>
> Message: 4
> Date: Fri, 14 Aug 2015 13:29:12 +0530
> From: Robin Jain <robinjain.chem.gmail.com>
> Subject: [AMBER] help in rdf
> To: amber <amber.ambermd.org>
> Message-ID:
> <CA+QHj+m18-h=
> wWF+MeO_RV7q1WRc-e8u-_Xi_3L0CToo0tRNuw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all , i have simulated 128 methanol molecule in a cubic box of 20.56
> ang. implies 0.787gm/cm3 system density.. Now i want to calculate pair
> correlation functions b/w methanol oxygen to methanol oxygen. For this i
> use following inputs
>
>
> *trajin X.mdcrd*
>
> *radial 1.dat 0.05 10 :MOH.O1 :MOH.O1 volume*
>
> *go*
> and
>
>
>
>
>
> *trajin X.mdcrdradial 1.dat 0.05 10 :MOH.O1 :MOH.O1 density
> 0.01481035625go*
>
> *(Density 0.01481035625 has been converted to molecule/ang.-3)*
> Now after using both input i got wrong g(r) value, when i look the
> literature value. so what is wrong with me, Please help me in this regard.
>
> --
> Robin Jain
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 14 Aug 2015 07:38:36 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] The protein is Leaving the water box!
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3qfTaQnUKicfsi=
> uR4NVEG5S5AahGs0kja5rH_Dtqm88Q.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Aug 13, 2015 at 8:36 PM, Amber mail <amber.auc14.gmail.com> wrote:
>
> > Dear AMBER users,
> >
> > I am performing a MD simulation using AMBER12 under the ff99SB force
> filed.
> > Initially, the structure was neutralized and then solvated using TIP3P
> > water model.
> >
> > After the minimization stage, a 50ps of MD simulation was performed from
> 0K
> > to 100K. The system is then heated up in increments of 25K with 50ps of
> MD
> > simulation at each temperature increment until the desired temperature of
> > 310K was established.
> >
> > This the control file for heating (0-100)K
> >
> > Heat
> > > &cntrl
> > > imin=0,
> > > ntx=1,
> > > irest=0,
> > > nstlim=25000,
> > > dt=0.002,
> > > ntf=2,
> > > ntc=2,
> > > tempi=0.0,
> > > temp0=100.0,
> > > ntpr=100,
> > > ntwx=100,
> > > cut=8.0,
> > > ntb=2,
> > > ntp=1,
> > > ntt=3,
> > > gamma_ln=1.0,
> > > tautp=1.0,
> > > taup=1.0,
> > > pres0=1.01325,
> > > nmropt=0,
> > > ig=-1,
> > > iwrap=1,
> > > /
> > >
> >
> > A 50 ns of MD simulation is going to be performed at 310K. Till now, I
> have
> > got 20 ns out of 50 ns. This is the control file for the production step
> >
> > Production
> > > &cntrl
> > > imin=0,
> > > ntx=5,
> > > irest=1,
> > > nstlim=5000000,
> > > dt=0.002,
> > > ntf=2,
> > > ntc=2,
> > > temp0=310.0,
> > > tempi=310.0,
> > > ntpr=5000,
> > > ntwx=5000,
> > > cut=8.0,
> > > ntb=2,
> > > ntp=1,
> > > ntt=3,
> > > gamma_ln=1.0,
> > > ig=-1,
> >
> > nmropt=0,
> > > iwrap=1,
> > > /
> > >
> >
> > The problem is that a part of the protein is leaving the water box after
> 20
> > ns of the MD production
> >
> >
> > ?
> > Please correct me If I am wrong, since I used the wrapping option
> > (iwrap=1), the water molecules should wrap (surround) any residue in case
> > if it is trying to leave the water box. does this mean that these outer
> > residues are being simulated now in vacuum?!
>
>
> ?No, this is not what it means. Your simulation is still being simulated
> under periodic boundary conditions, which means that *all of space* is
> filled with copies of particles translated by whole periodic box vectors.
> Consider a basic cartoon of periodic boundary conditions (e.g.,
> http://dynamomd.org/images/PBC.png). Note that in that image, there are
> an
> *infinite* number of choices you can make about how to define the "primary
> box". You can translate it arbitrarily in both dimensions (all three
> dimensions if you have a 3-D periodic system, like in MD simulations) so
> that it cuts through the middle of any of the circles.
>
> One way to define the periodic cell is to put the protein in the center and
> all of the water around it. That is probably what you would most like to
> see, but that's no more "correct" from a simulation perspective than
> translating the box so that the center of mass of the protein is next to
> one of the edges (which means that part of the protein appears to "stick
> out" of the primary unit cell). If you want a different view, you need to
> image your trajectory to achieve it. For 99% of applications, the
> "autoimage" command in cpptraj will give you the "prettiest" unit cell
> representation.
> ?
>
>
> > If I am right, is setting
> > ntb=2 (boundary conditions) works for this behavior, and there is no
> > problem ?!
> >
>
> ?No. ntb=2 simply means "use periodic boundary conditions, but let the
> unit cell change size and maybe shape". This happens when you run constant
> pressure simulations. Periodic boundary conditions are periodic boundary
> conditions, whether you set ntb=1 or ntb=2, there's no difference in this
> regard.
> ?
>
> > Another question regarding the heating stage, below is the plot of
> > Temperature vs. Time before production, I am wondering why the increase
> in
> > the Temperature was not going smoothly and the equilibration did not
> reach
> > at the end of the heating stage (like the results of the tutorials,
> which I
> > performed before)
> >
> >
> > ?A same pattern (sudden change) was also obtained for the Potential
> energy,
> > Kinetic Energy and the Total Energy (in the heating stage)
> >
>
> ?That is because the heating occurs rapidly at the start of each stage.
> Generally this isn't a huge problem, but you can use nmropt=1 with
> temperature control to slowly vary the target temperature in order to heat
> the system steadily from low to high temperature in a single simulation.
> There are examples (called "slow heat") in my input file repository at
> https://github.com/swails/Mdins
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 14 Aug 2015 07:46:27 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Job submission script for SGE
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3qWC+eRnMFUHG+dgzZsjbrLi0KPtvO=
> 5ahy6xV1ubUPHg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Aug 13, 2015 at 7:50 PM, Himansu <himansubiswal.gmail.com> wrote:
>
> > Dear Amber users,
> > Recently we installed AMBER14 and AMBER TOOLS 15 in our SGE HPC. We
> are
> > using Tutorials to verify the installation.
>
>
> ?Don't use the tutorials simply to verify the installation -- that's what
> the test suite is for. The manual has instructions on running the test
> suite.?
>
> Currently we are using
> > Tutorial: A room-temperature ionic liquid. The serial one is working but
> > not the parallel one. I am attaching the job submission script (AMBER.sh)
> > that I used for the parallel run for other software such as TURBOMOLE.
> > Seeking your suggestions in this regard.
> >
>
> ?Your submission script is *way* too complicated. What's more is that you
> are running all steps -- including the setup steps -- in the compute node.
> The "typical" workflow is to do the first steps by hand on your workstation
> (or interactively on the login node) -- preparing the PDB file, running
> leap to get the prmtop and inpcrd file -- and then use a submission script
> to run either sander or pmemd (perhaps several sander or pmemd jobs
> consecutively).
>
> ?Also, clusters like the one you are trying to run on are all different. I
> suggest consulting your cluster documentation for how to run
> MPI-parallelized programs (in general, you will need some kind of "mpirun"
> or "mpiexec" command to run sander.MPI or pmemd.MPI with more than one
> processor). Also try simplifying your submission script significantly so
> that it only runs a single sander.MPI simulation and see if you can get it
> to work. That will be easier both for you to debug and for us to help
> with? if you still have problems.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 7
> Date: Fri, 14 Aug 2015 13:46:34 +0200
> From: Gerald Monard <Gerald.Monard.univ-lorraine.fr>
> Subject: Re: [AMBER] Job submission script for SGE
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <55CDD51A.6030306.univ-lorraine.fr>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hi,
>
> From your script, I can see at least one problem: you don't use the
> DO_PARALLEL variable. Try to replace the line "sander.MPI -O ..." by
> "$DO_PARALLEL sander.MPI -O ...".
>
> Sincerely,
>
> Gerald.
>
> On 08/14/2015 01:50 AM, Himansu wrote:
> > Dear Amber users,
> > Recently we installed AMBER14 and AMBER TOOLS 15 in our SGE HPC. We
> are
> > using Tutorials to verify the installation. Currently we are using
> > Tutorial: A room-temperature ionic liquid. The serial one is working but
> > not the parallel one. I am attaching the job submission script (AMBER.sh)
> > that I used for the parallel run for other software such as TURBOMOLE.
> > Seeking your suggestions in this regard.
> >
> > Best regards,
> > Himansu
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
>
> ____________________________________________________________________________
>
> Prof. Gerald MONARD
> SRSMC, Universit? de Lorraine, CNRS
> Boulevard des Aiguillettes B.P. 70239
> F-54506 Vandoeuvre-les-Nancy, FRANCE
>
> e-mail : Gerald.Monard.univ-lorraine.fr
> tel. : +33 (0)383.684.381
> fax : +33 (0)383.684.371
> web : http://www.monard.info
>
>
> ____________________________________________________________________________
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Fri, 14 Aug 2015 14:11:25 +0200
> From: Amber mail <amber.auc14.gmail.com>
> Subject: Re: [AMBER] The protein is Leaving the water box!
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAJAn0fi6v3dh-xsLu-BBC9gTrKgdg4iXVY-FpFEDqOSMR6ckHw.mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Thanks a lot for your help !
>
> So you advice me to continue the simulation.
>
> By the way, I've just finished another 10 ns of MD production, and attached
> below is a screen shot of the water box after 30 ns MD production
> I don't know why this gap on the right side of the water box was created..?
>
>
> ?
> Thanks a lot for your time!
>
>
> On Fri, Aug 14, 2015 at 1:38 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Thu, Aug 13, 2015 at 8:36 PM, Amber mail <amber.auc14.gmail.com>
> wrote:
> >
> > > Dear AMBER users,
> > >
> > > I am performing a MD simulation using AMBER12 under the ff99SB force
> > filed.
> > > Initially, the structure was neutralized and then solvated using TIP3P
> > > water model.
> > >
> > > After the minimization stage, a 50ps of MD simulation was performed
> from
> > 0K
> > > to 100K. The system is then heated up in increments of 25K with 50ps of
> > MD
> > > simulation at each temperature increment until the desired temperature
> of
> > > 310K was established.
> > >
> > > This the control file for heating (0-100)K
> > >
> > > Heat
> > > > &cntrl
> > > > imin=0,
> > > > ntx=1,
> > > > irest=0,
> > > > nstlim=25000,
> > > > dt=0.002,
> > > > ntf=2,
> > > > ntc=2,
> > > > tempi=0.0,
> > > > temp0=100.0,
> > > > ntpr=100,
> > > > ntwx=100,
> > > > cut=8.0,
> > > > ntb=2,
> > > > ntp=1,
> > > > ntt=3,
> > > > gamma_ln=1.0,
> > > > tautp=1.0,
> > > > taup=1.0,
> > > > pres0=1.01325,
> > > > nmropt=0,
> > > > ig=-1,
> > > > iwrap=1,
> > > > /
> > > >
> > >
> > > A 50 ns of MD simulation is going to be performed at 310K. Till now, I
> > have
> > > got 20 ns out of 50 ns. This is the control file for the production
> step
> > >
> > > Production
> > > > &cntrl
> > > > imin=0,
> > > > ntx=5,
> > > > irest=1,
> > > > nstlim=5000000,
> > > > dt=0.002,
> > > > ntf=2,
> > > > ntc=2,
> > > > temp0=310.0,
> > > > tempi=310.0,
> > > > ntpr=5000,
> > > > ntwx=5000,
> > > > cut=8.0,
> > > > ntb=2,
> > > > ntp=1,
> > > > ntt=3,
> > > > gamma_ln=1.0,
> > > > ig=-1,
> > >
> > > nmropt=0,
> > > > iwrap=1,
> > > > /
> > > >
> > >
> > > The problem is that a part of the protein is leaving the water box
> after
> > 20
> > > ns of the MD production
> > >
> > >
> > > ?
> > > Please correct me If I am wrong, since I used the wrapping option
> > > (iwrap=1), the water molecules should wrap (surround) any residue in
> case
> > > if it is trying to leave the water box. does this mean that these outer
> > > residues are being simulated now in vacuum?!
> >
> >
> > ?No, this is not what it means. Your simulation is still being simulated
> > under periodic boundary conditions, which means that *all of space* is
> > filled with copies of particles translated by whole periodic box vectors.
> > Consider a basic cartoon of periodic boundary conditions (e.g.,
> > http://dynamomd.org/images/PBC.png). Note that in that image, there are
> > an
> > *infinite* number of choices you can make about how to define the
> "primary
> > box". You can translate it arbitrarily in both dimensions (all three
> > dimensions if you have a 3-D periodic system, like in MD simulations) so
> > that it cuts through the middle of any of the circles.
> >
> > One way to define the periodic cell is to put the protein in the center
> and
> > all of the water around it. That is probably what you would most like to
> > see, but that's no more "correct" from a simulation perspective than
> > translating the box so that the center of mass of the protein is next to
> > one of the edges (which means that part of the protein appears to "stick
> > out" of the primary unit cell). If you want a different view, you need
> to
> > image your trajectory to achieve it. For 99% of applications, the
> > "autoimage" command in cpptraj will give you the "prettiest" unit cell
> > representation.
> > ?
> >
> >
> > > If I am right, is setting
> > > ntb=2 (boundary conditions) works for this behavior, and there is no
> > > problem ?!
> > >
> >
> > ?No. ntb=2 simply means "use periodic boundary conditions, but let the
> > unit cell change size and maybe shape". This happens when you run
> constant
> > pressure simulations. Periodic boundary conditions are periodic boundary
> > conditions, whether you set ntb=1 or ntb=2, there's no difference in this
> > regard.
> > ?
> >
> > > Another question regarding the heating stage, below is the plot of
> > > Temperature vs. Time before production, I am wondering why the increase
> > in
> > > the Temperature was not going smoothly and the equilibration did not
> > reach
> > > at the end of the heating stage (like the results of the tutorials,
> > which I
> > > performed before)
> > >
> > >
> > > ?A same pattern (sudden change) was also obtained for the Potential
> > energy,
> > > Kinetic Energy and the Total Energy (in the heating stage)
> > >
> >
> > ?That is because the heating occurs rapidly at the start of each stage.
> > Generally this isn't a huge problem, but you can use nmropt=1 with
> > temperature control to slowly vary the target temperature in order to
> heat
> > the system steadily from low to high temperature in a single simulation.
> > There are examples (called "slow heat") in my input file repository at
> > https://github.com/swails/Mdins
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 9
> Date: Fri, 14 Aug 2015 09:00:11 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] The protein is Leaving the water box!
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3rXo-o6obETEc+OvXMrd4+5rc=
> Mo80K-W+UUa7qSiuJ2w.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Fri, Aug 14, 2015 at 8:11 AM, Amber mail <amber.auc14.gmail.com> wrote:
>
> > Thanks a lot for your help !
> >
> > So you advice me to continue the simulation.
> >
> > By the way, I've just finished another 10 ns of MD production, and
> attached
> > below is a screen shot of the water box after 30 ns MD production
> > I don't know why this gap on the right side of the water box was
> created..?
> >
>
> ?This is, again, the effect of periodic boundary conditions. Half of the
> protein is sticking out of one side of the unit cell into the adjacent
> one. Which means that its periodic image has half of *its* protein
> sticking into *that* unit cell.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 10
> Date: Fri, 14 Aug 2015 09:47:07 -0600
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] help in rdf
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOYcf3rUOfUAzBsjyBKRA7N-g=QyMcpsXFdp=
> FC_Hr9Mrw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Fri, Aug 14, 2015 at 1:59 AM, Robin Jain <robinjain.chem.gmail.com>
> wrote:
> > *(Density 0.01481035625 has been converted to molecule/ang.-3)*
> > Now after using both input i got wrong g(r) value, when i look the
> > literature value. so what is wrong with me, Please help me in this
> regard.
>
> Without knowing what MeOH parameters you used and how you ran your
> simulations we can only speculate. Maybe the parameters you used
> aren't ideal. Tough to say without more information.
>
> -Dan
>
> >
> > --
> > Robin Jain
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
>
>
> ------------------------------
>
> Message: 11
> Date: Fri, 14 Aug 2015 13:45:56 -0400
> From: Investigador Qu?mica <investigacion.faq.gmail.com>
> Subject: [AMBER] the better box size
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAGBLR-VBz7GoVLzKzCv8MazBjf31ywzaR_toX7NOJs2rd7PUXg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Sirs:
>
> Could you please help me to set up the better box size for AMBER
> calculation.
>
> We have used solvateoct with 8.0 , 9.0 , 10.0 and 11.0. And we get
> different Etot values.
>
> Thank you.
>
> Best regards
>
> --
> ?rea de Software
> Investigaci?n Facultad de Qu?mica
> Universidad de Santiago de Chile
>
>
> ------------------------------
>
> Message: 12
> Date: Fri, 14 Aug 2015 14:12:20 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] the better box size
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3qN83Tb9F9GgWv0a14+KFg7S0KZhSj_mf9_k9w=
> V-REsQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Fri, Aug 14, 2015 at 1:45 PM, Investigador Qu?mica <
> investigacion.faq.gmail.com> wrote:
>
> > Dear Sirs:
> >
> > Could you please help me to set up the better box size for AMBER
> > calculation.
> >
>
> ?Define "better".
> ?
>
> > We have used solvateoct with 8.0 , 9.0 , 10.0 and 11.0. And we get
> > different Etot values.
> >
>
> ?Of course you do. Energy is an extensive property, so it depends on the
> number of particles in your simulation.
> ??
> ?There are offsetting costs between smaller and larger solvent boxes.
> Smaller boxes are more likely to yield artifacts due to periodic images of
> the solute interacting with each other (and other effects associated with
> the much higher effective concentrations). Larger boxes have more atoms
> (obviously), and so you can't sample as much as you can with a smaller
> box. Somewhere between 10 and 15 Angstroms is typically a fine choice,
> although it's not appropriate for all applications.
>
> The bigger your box, the "better" your simulation, since it reduces
> periodicity artifacts. The smaller your box, the "better" your sampling,
> since it has fewer atoms. "best" is some undetermined compromise between
> the two.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1311, Issue 1
> **************************************
>



-- 
Robin Jain




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Received on Sat Aug 15 2015 - 02:00:03 PDT
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