Thanks everyone for your help on this issue. I'd like to provide an update
for posterity: the problem turned out to be caused by using a version of
Amber20 that did not have all of the latest patches installed (in
particular, Amber20 patch 8, I believe).
Now that I have the patch installed I'm getting excellent stability. Thanks
to Dr. Simmerling for suggesting this fix!
On Thu, Mar 11, 2021 at 3:01 PM <amber-request.ambermd.org> wrote:
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: pmemd.cuda unstable with ff19SB+OPC and HMassRepartition
> (Carlos Simmerling)
> 2. Re: makeDIST_RST (Ming Tang)
> 3. Secstruct error (Kodituwakku,Dimuthu Nirmani)
> 4. sander/orca/xtb ?Low parallel efficiency (wangjianing_mail)
> 5. Re: pmemd.cuda unstable with ff19SB+OPC and HMassRepartition
> (Gerald Monard)
> 6. GPU installation error amber18 (Renato Araujo)
> 7. Re: pmemd.cuda unstable with ff19SB+OPC and HMassRepartition
> (David A Case)
> 8. Re: GPU installation error amber18 (David A Case)
> 9. Re: sander/orca/xtb ?Low parallel efficiency (Adrian Roitberg)
> 10. Re: Problem with CG minimization in implicit solvent
> (Adrian Roitberg)
> 11. constant ph md (Abhik Ghosh Moulick)
> 12. Re: constant ph md (Adrian Roitberg)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 10 Mar 2021 15:52:30 -0500
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Subject: Re: [AMBER] pmemd.cuda unstable with ff19SB+OPC and
> HMassRepartition
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAGk3s-Q6G8eRVEOO1cF-33H-MZLWSayk88a4kTNuoshFnFW4+A.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> a couple quick things to check:
> 1) when you built the system in leap, did you load the OPC libraries AFTER
> the ff19SB library?
> 2) there was a patch in some of the code that is used with CMAPS, is your
> AMber20 up to date with patches?
>
>
> On Wed, Mar 10, 2021 at 2:27 PM Tucker Burgin <tburgin.uw.edu> wrote:
>
> > Hi Amber users,
> >
> > I'm trying to develop a workflow for high-throughput simulations of
> > proteins. I've got an enzyme-substrate complex parameterized with ff19SB
> in
> > a box of OPC waters, to which I've applied hydrogen mass repartitioning
> > using ParmEd with the default settings. I minimized, heated from 100 to
> 300
> > K, and equilibrated for 1 ns using pmemd.MPI, and all that is very
> > well-behaved.
> >
> > Now I'm trying to run longer simulations with the equilibrated structure
> > using pmemd.cuda, but whenever I try to run a simulation with a timestep
> > longer than 2 fs, it runs for a while (anywhere from a few hundred ps to
> > several ns) before crashing with a generic error message:
> >
> > cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> > encountered
> >
> > This happens very consistently. I do *not *have this problem if I reduce
> > the timestep to 2 fs, but I don't understand why. I have confirmed that
> the
> > hydrogen mass repartitioning is correctly reflected in the topology file,
> > and SHAKE is turned on. I have tried manually restarting the crashed
> > simulation many times thinking that it maybe just needed more
> > equilibration, but after several restarts I'm seeing no improvement.
> Here's
> > my input file:
> >
> > &cntrl
> >
> > imin=0,
> >
> > ioutfm=1,
> >
> > ntx=1,
> >
> > ntxo=1,
> >
> > nstlim=2500000,
> >
> > dt=0.004,
> >
> > ntf=2,
> >
> > ntc=2,
> >
> > tempi=300.0,
> >
> > temp0=300.0,
> >
> > ntpr=25000,
> >
> > ntwx=25000,
> >
> > cut=8.0,
> >
> > ntb=2,
> >
> > ntp=1,
> >
> > ntt=2,
> >
> > vrand=10000,
> >
> > ig=-1,
> >
> > taup=2,
> >
> > &end
> >
> > As a further test, I have tried removing the substrate from the model
> > altogether, leaving only a protein consisting entirely of standard
> > residues, a single sodium ion, and the OPC water molecules, and still the
> > problem persists.
> >
> > The output files look fine, with reasonable values for the temperature,
> all
> > the energy terms, and the density. The only indication I have of anything
> > weird in the output files is that the temperature at the 0th step is
> always
> > about 436 K (even though tempi is 300 K and the system has been
> > equilibrated at that temperature), but it returns to about 300 K by the
> > next write to the output file. Here's an example output line from step 0:
> >
> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 436.04 PRESS =
> > -19.0
> >
> > Etot = -151011.7523 EKtot = 47799.7254 EPtot =
> > -198811.4778
> >
> > BOND = 1683.1249 ANGLE = 4073.2499 DIHED =
> > 2465.2522
> >
> > UB = 0.0000 IMP = 0.0000 CMAP =
> > 381.8329
> >
> > 1-4 NB = 1689.6414 1-4 EEL = 19887.1333 VDWAALS =
> > 21224.1537
> >
> > EELEC = -250215.8661 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> >
> > EKCMT = 13861.9920 VIRIAL = 14078.6721 VOLUME =
> > 527955.5220
> >
> > Density =
> > 1.0336
> >
> > There's nothing obviously weird to my eye going on in the simulation
> > trajectory. I'm using Amber 20. Since I can't find anything wrong with
> the
> > simulations I'm considering just writing a script to automatically
> restart
> > my simulations whenever they crash, but I'd feel a lot more comfortable
> if
> > I knew for sure what the problem was. Anyone have any ideas or
> suggestions?
> > Please let me know if there's any more information I can provide.
> >
> > Thanks!
> > -Tucker Burgin
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 11 Mar 2021 01:39:08 +0000
> From: Ming Tang <m21.tang.qut.edu.au>
> Subject: Re: [AMBER] makeDIST_RST
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> SYXPR01MB06219D16CB64FBBFAFD20D70B6909.SYXPR01MB0621.ausprd01.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Daniel,
>
> It worked for 29 heavy atoms in each group! Why do hydrogens make trouble?
>
> thanks,
> Ming
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Wednesday, 10 March 2021 9:36 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] makeDIST_RST
>
> Try excluding hydrogens from the groups.
>
> On Tue, Mar 9, 2021 at 5:51 PM Ming Tang <m21.tang.qut.edu.au> wrote:
>
> > Hi David,
> >
> > Thanks a lot for your guidance. The problem was that there were too many
> > elements (35 each) in the IGR1, IGR2 arrays.
> >
> > May I ask is there a command in Amber that can insert a number of
> > molecules in a solvated protein box just like the insert-molecules
> command
> > in Gromacs and packmol? I tried to treat my molecules as ions and use
> > addions command. The molecules were added successfully and they are all
> > placed outside of the solvated box and very far away from the protein.
> >
> > Many thanks,
> > Ming
> >
> >
> >
> > ________________________________
> > From: David A Case <david.case.rutgers.edu>
> > Sent: Sunday, 7 March 2021 11:06 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] makeDIST_RST
> >
> > On Sun, Mar 07, 2021, Ming Tang wrote:
> > >
> > >Thanks for the precious guidance. This what I want and the script was
> > >perfect. But I after 4000 steps the production run got this error:
> > >cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> > >encountered. And there is not restrain in the output as below:
> > >
> > >wrapping first mol.: 30.51583 43.15591 74.74821
> > >wrapping first mol.: 30.51583 43.15591 74.74821
> > >
> > > NSTEP = 4000 TIME(PS) = 608.000 TEMP(K) = 308.07 PRESS =
> > -237.6
> > > Etot = -153810.1794 EKtot = 36112.7344 EPtot =
> > -189922.9138
> > > BOND = 578.5793 ANGLE = 1445.0337 DIHED =
> > 2202.2790
> > > 1-4 NB = 687.3814 1-4 EEL = 7970.8282 VDWAALS =
> > 24116.2997
> > > EELEC = -226923.3149 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > > EKCMT = 17106.3674 VIRIAL = 20136.3763 VOLUME =
> > 590645.1967
> > > Density =
> > 0.9997
> > >
> >
> ------------------------------------------------------------------------------
> > >
> > > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
> 0.000
> >
> > A zero restraint energy probably just means that all the restraints are
> > satisfied, that is, that the average distance being restrained is greater
> > than 1.8 ?.
> >
> > >
> > >&rst iat=-1,-1,0
> > > r1=1.300000, r2=1.800000, r3=10.000000, r4=10.500000, rk2=20.000000,
> > rk3=0.000000,
> > > IGR1(1)=2794,IGR1(2)=2795,IGR1(3)=2796,...
> > > IGR2(1)=2829,IGR2(2)=2830,IGR2(3)=2831,...
> > > nstep1=0, nstep2=0,
> > > &end
> >
> > Since you set rk3=0, this is just a lower bound. That is fine if it what
> > you want.
> >
> > > nstlim=2000000000,dt=0.002,
> >
> > Debugging steps:
> >
> > 1. Since the restraints aren't doing anything anyway, run a short
> > simulation (say 10000 steps, not 2 billion!) and see if you still get the
> > crash.
> >
> > 2. Set iwrap=0 (you should be doing this anyway). It's certainly
> possible
> > that the restraints get confused when wrapping is going on.
> >
> > 3. If the problem seems to be with the restraints, try a test run with
> > many
> > fewer elements in the IGR1, IGR2 arrays. It's not clear how big those
> > arrays are, but there may be some upper bound.
> >
> > 4. Try setting ntb=1, ntp=0 to see if there is something odd about
> > pressure.
> >
> > > ntpr=1000, ntwx=1000,ntwr=1000,iwrap=1,
> >
> > Note that if this job actually ran, you would probably exhaust all disk
> > space: you are asking to dump a trajectory every 1000 steps, so you would
> > get 2000000000/1000 = 2 million frames in your trajectory file(!)
> >
> > ...good luck...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
> >
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!NVzLfOphnbDXSw!U6eOcd5HrgtEPZGiASQIbF3SHRWZccne80DUrVfBwxJkS3uY0EfbF_52zmvPTebbKiWk$
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!NVzLfOphnbDXSw!W3bL0pz88XqV7L-l0TDZmF9CBMwfp2JrdL3UINWhl2k0LkkcHwGIUEXBX9fCGR4zycED$
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!NVzLfOphnbDXSw!W3bL0pz88XqV7L-l0TDZmF9CBMwfp2JrdL3UINWhl2k0LkkcHwGIUEXBX9fCGR4zycED$
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 11 Mar 2021 03:48:34 +0000
> From: "Kodituwakku,Dimuthu Nirmani" <dkodituwakku.ufl.edu>
> Subject: [AMBER] Secstruct error
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <
> BN6PR22MB0740B29B71FC47835B7390A2D0909.BN6PR22MB0740.namprd22.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I'm using secstruct on cpptraj to analyze the secondary structure of my
> trajectory. It produces an error "Error: Too many bridges for 248 (to 54)".
> I'm using cpptraj on Amber/20 and charmm forcefields. The command I used
> for my calculation is "secstruct :1-587 out dssp.gnu nameh HN ".
>
> Any help would be greatly appreciated!
>
> Thank you,
>
> -Dimuthu
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 11 Mar 2021 12:12:58 +0800 (GMT+08:00)
> From: wangjianing_mail <wangjianing_mail.163.com>
> Subject: [AMBER] sander/orca/xtb ?Low parallel efficiency
> To: amber <amber.ambermd.org>
> Message-ID:
> <4b8b8d12.5eff.1781f7cd77e.Coremail.wangjianing_mail.163.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Amber user:
>
>
> I successfully used the gfn-xTB in amber QM/MM, by modifying
> sander/qm2_extern_orc_module.F90, but low parallel efficiency problem
> appeared.
> However both 'num_threads=12' in orc namelist of amber input file ?'%pal
> NPROCS 12 end' in orc_job.tpl and 'export OMP/MVK_NUM_THREADS' can not be
> efficiently parallel.
>
>
> Both scheme can only increase the speed by up to about 10% than 1 core
> scheme, and even reduce the computational efficiency, I think this is
> abnormal. Can someone give me any help here?
>
>
> #SI
> software: Amber18(gnu openmpi) openmpi 3.1.4 orca 4.2.1 gcc 4.8.5 openMP
> 201107
> test reslut
>
> method orc-num_threadsxtb-pal NPORCS OPENMP ps/d
> xtb 1 1 164
> xtb 1 1 1267
> xtb 12 1 163
> xtb 1 12 121.8
> b3lyp 1 1 /0.17
> b3lyp 20 1 /0.17
> b3lyp 1 20 / 1.83
> Regards,
> Jia-Ning Wang
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 11 Mar 2021 20:47:07 +0900
> From: Gerald Monard <gerald.monard.gmail.com>
> Subject: Re: [AMBER] pmemd.cuda unstable with ff19SB+OPC and
> HMassRepartition
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEWHimyXyYN3dMdkedmQZsdEQHdK10=
> wfWeMObzixSBWfzadjg.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
> If I may: put ntf=1.
> IMHO the problem is that you don't compute the harmonic spring on the bonds
> involving hydrogen. In a perfect world, no problem. But because here the dt
> is a little bit high you can end up with situations where shake has some
> problem to recover the correct geometries, and then things can quickly go
> bad.
> It happen to me several times and ntf=1 is really a must for me. That won't
> affect the speed of your simulations.
> Also, if your system is not very much "equilibrated: at the beginning,
> vrand=10000 is may be also too much. The default vrand=1000 should be
> sufficient to reset the temperature at the beginning of the simulations and
> stay at 300K.
>
> Hope it helps,
>
> Gerald.
>
> On Thu, Mar 11, 2021 at 4:26 AM Tucker Burgin <tburgin.uw.edu> wrote:
>
> > Hi Amber users,
> >
> > I'm trying to develop a workflow for high-throughput simulations of
> > proteins. I've got an enzyme-substrate complex parameterized with ff19SB
> in
> > a box of OPC waters, to which I've applied hydrogen mass repartitioning
> > using ParmEd with the default settings. I minimized, heated from 100 to
> 300
> > K, and equilibrated for 1 ns using pmemd.MPI, and all that is very
> > well-behaved.
> >
> > Now I'm trying to run longer simulations with the equilibrated structure
> > using pmemd.cuda, but whenever I try to run a simulation with a timestep
> > longer than 2 fs, it runs for a while (anywhere from a few hundred ps to
> > several ns) before crashing with a generic error message:
> >
> > cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> > encountered
> >
> > This happens very consistently. I do *not *have this problem if I reduce
> > the timestep to 2 fs, but I don't understand why. I have confirmed that
> the
> > hydrogen mass repartitioning is correctly reflected in the topology file,
> > and SHAKE is turned on. I have tried manually restarting the crashed
> > simulation many times thinking that it maybe just needed more
> > equilibration, but after several restarts I'm seeing no improvement.
> Here's
> > my input file:
> >
> > &cntrl
> >
> > imin=0,
> >
> > ioutfm=1,
> >
> > ntx=1,
> >
> > ntxo=1,
> >
> > nstlim=2500000,
> >
> > dt=0.004,
> >
> > ntf=2,
> >
> > ntc=2,
> >
> > tempi=300.0,
> >
> > temp0=300.0,
> >
> > ntpr=25000,
> >
> > ntwx=25000,
> >
> > cut=8.0,
> >
> > ntb=2,
> >
> > ntp=1,
> >
> > ntt=2,
> >
> > vrand=10000,
> >
> > ig=-1,
> >
> > taup=2,
> >
> > &end
> >
> > As a further test, I have tried removing the substrate from the model
> > altogether, leaving only a protein consisting entirely of standard
> > residues, a single sodium ion, and the OPC water molecules, and still the
> > problem persists.
> >
> > The output files look fine, with reasonable values for the temperature,
> all
> > the energy terms, and the density. The only indication I have of anything
> > weird in the output files is that the temperature at the 0th step is
> always
> > about 436 K (even though tempi is 300 K and the system has been
> > equilibrated at that temperature), but it returns to about 300 K by the
> > next write to the output file. Here's an example output line from step 0:
> >
> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 436.04 PRESS =
> > -19.0
> >
> > Etot = -151011.7523 EKtot = 47799.7254 EPtot =
> > -198811.4778
> >
> > BOND = 1683.1249 ANGLE = 4073.2499 DIHED =
> > 2465.2522
> >
> > UB = 0.0000 IMP = 0.0000 CMAP =
> > 381.8329
> >
> > 1-4 NB = 1689.6414 1-4 EEL = 19887.1333 VDWAALS =
> > 21224.1537
> >
> > EELEC = -250215.8661 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> >
> > EKCMT = 13861.9920 VIRIAL = 14078.6721 VOLUME =
> > 527955.5220
> >
> > Density =
> > 1.0336
> >
> > There's nothing obviously weird to my eye going on in the simulation
> > trajectory. I'm using Amber 20. Since I can't find anything wrong with
> the
> > simulations I'm considering just writing a script to automatically
> restart
> > my simulations whenever they crash, but I'd feel a lot more comfortable
> if
> > I knew for sure what the problem was. Anyone have any ideas or
> suggestions?
> > Please let me know if there's any more information I can provide.
> >
> > Thanks!
> > -Tucker Burgin
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 11 Mar 2021 09:53:14 -0300
> From: Renato Araujo <renatoacufpa.gmail.com>
> Subject: [AMBER] GPU installation error amber18
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CALoSBpgZkzd5LLpwF2N3CsS5kPLLc7zO+e3KHKJYKy5qgq3SUQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear amber users
>
> I am trying to install amber18 on GPU, but I am getting the following error
> after step
>
> ./configure -cuda gnu
>
> Your AMBERHOME environment variable is not set! Auto set it to:
>
> /usr/local/chem/amber18
>
> Checking for updates...
>
> Checking for available patches online. This may take a few seconds...
>
> Available AmberTools 19 patches:
>
> No patches available
>
> Available Amber 18 patches:
>
> No patches available
>
> AMBER_PREFIX=/usr/local/chem/amber18
>
> AMBER_SOURCE=/usr/local/chem/amber18
>
> Using the AmberTools miniconda installation in
> /usr/local/chem/amber18/miniconda
>
> version 2.7.16
>
> Error: CUDA_HOME is not set. This must point to your NVIDIA tools
> installation
>
> Configure failed due to the errors above!
>
>
>
> Please I need help
>
> Thanks
> --
> Prof Dr Renato Costa
> Instituto Federal do Par? - IFPA
> Grupo de Modelagem Molecular - UFPA
> Tel.+55 91 985484622
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 11 Mar 2021 08:48:30 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] pmemd.cuda unstable with ff19SB+OPC and
> HMassRepartition
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20210311134830.7ttmzndrt3yf76tt.godel.fios-router.home>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Thu, Mar 11, 2021, Gerald Monard wrote:
>
> >If I may: put ntf=1.
>
> Also: set the SHAKE tolerance to 1.d-6.
>
> It would be of interest to know if the problem persists when setting ntt=3.
> I think ntt=2 has not been so widely tested.
>
> Given previous reports, it would also be of interest to know if the problem
> persists if you use ff14SB in place of ff19SB.
>
> I'm only suggesting the above for tests, to help try to narrow down the
> combination of parameters that leads to the behavior you report.
>
> ...thanks...dac
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 11 Mar 2021 08:54:22 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] GPU installation error amber18
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20210311135422.ubfuowoogdvowswm.godel.fios-router.home>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Thu, Mar 11, 2021, Renato Araujo wrote:
>
> >Error: CUDA_HOME is not set. This must point to your NVIDIA tools
> >installation
>
> You need to find where the CUDA SDK is installed on your system. This is
> usually in /usr/local/cuda, or perhaps /usr/local/cuda-xx.x, but it could
> be
> somewhere very different. Try typing "which nvcc", then use the part
> before the "/bin/nvcc".
>
> ...good luck...dac
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Thu, 11 Mar 2021 09:11:30 -0500
> From: Adrian Roitberg <roitberg.ufl.edu>
> Subject: Re: [AMBER] sander/orca/xtb ?Low parallel efficiency
> To: <amber.ambermd.org>
> Message-ID: <725a028e-b018-28b4-7498-984be650c9f3.ufl.edu>
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>
> You should first try to run gfn-xtb alone and see if that parallelizes
> for a system like yours, specially the size.
>
> I doubt that gfn-xtb would really parallelize over many cores, unless
> you have a pretty large QM system.
>
> Adrian
>
>
> On 3/10/21 11:12 PM, wangjianing_mail wrote:
> > [External Email]
> >
> > Dear Amber user:
> >
> >
> > I successfully used the gfn-xTB in amber QM/MM, by modifying
> sander/qm2_extern_orc_module.F90, but low parallel efficiency problem
> appeared.
> > However both 'num_threads=12' in orc namelist of amber input file
> ?'%pal NPROCS 12 end' in orc_job.tpl and 'export OMP/MVK_NUM_THREADS' can
> not be efficiently parallel.
> >
> >
> > Both scheme can only increase the speed by up to about 10% than 1 core
> scheme, and even reduce the computational efficiency, I think this is
> abnormal. Can someone give me any help here?
> >
> >
> > #SI
> > software: Amber18(gnu openmpi) openmpi 3.1.4 orca 4.2.1 gcc 4.8.5
> openMP 201107
> > test reslut
> >
> > method orc-num_threadsxtb-pal NPORCS OPENMP ps/d
> > xtb 1 1 164
> > xtb 1 1 1267
> > xtb 12 1 163
> > xtb 1 12 121.8
> > b3lyp 1 1 /0.17
> > b3lyp 20 1 /0.17
> > b3lyp 1 20 / 1.83
> > Regards,
> > Jia-Ning Wang
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
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>
> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Thu, 11 Mar 2021 10:36:49 -0500
> From: Adrian Roitberg <roitberg.ufl.edu>
> Subject: Re: [AMBER] Problem with CG minimization in implicit solvent
> To: <amber.ambermd.org>
> Message-ID: <b22f8a32-8c57-15c2-d074-537b49537cba.ufl.edu>
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>
> For what is worth, I managed to reproduce this effect, even using igb=6,
> in vacuo, so this is not a gb issue.
>
> Steepest descent all the way does not display this problem.
>
>
> Adrian
>
>
>
> On 3/10/21 2:17 PM, Alejandro Gil Ley wrote:
> > [External Email]
> >
> > Dear Amber Community
> >
> > I found a peculiar pattern in the forces and energy as a function of the
> minimization steps while running minimizations with pmemd and sander using
> conjugate gradient in implicit solvent, in Amber20.
> > After the first initial steps using steepest descent, CG energies and
> forces exhibited frequent jumps of several orders of magnitude as the
> minimization progressed.
> > To demonstrate this issue here I used alanine-dipeptide. All the input
> files needed to reproduce this data are attached.
> > I tried different systems, like DNA and TRP cage, and changed the
> frequency of nonbonded list updates nsnb, but the problem remained.
> >
> > Below I have plotted, as a function of the minimization step, the
> maximum force and the difference between the system energy and the minimum
> energy (plus a constant).
> > For this example I used ntmin = 1, ncyc = 100, nsnb = 25 and cut = 9999.
> You can see that energies decrease monotonically for the first 100 steepest
> descent steps,
> > but then immediately after, frequent jumps in forces and energy of
> several orders of magnitude appear. Example is shown for pmemd and sander.
> > If the xmin minimizer is used with PRCG then the issue disappears.
> >
> > I could do a full minimization using steepest descent and ignore this
> problem,
> > but I would like to know whether someone has encountered this problem
> before.
> > Is this a known issue with conjugate gradient in implicit solvent?
> >
> > Thanks in advanced for your help,
> >
> > Alejandro Gil
> >
> >
> >
> > [A picture containing background pattern Description automatically
> generated]<
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.zymeworks.com_&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=5HtdyQdtA3h7fbFBQUBD3rv7lzkeARRHo2c29ccoIwI&s=sVflC2MeqOgJCZDEly4dM5jPVFl-D8CI6j7WQcpAnxE&e=
> >
> >
> > Alejandro Gil Ley, PhD (he / him)
> >
> > Scientist, Molecular Simulations
> >
> > Office: (604) 555-1234 ext. 1033
> >
> > alejandro.gilley.zymeworks.com<mailto:diana.papove.zymeworks.com>
> >
> > 1385 West 8th Avenue, Suite 540 | Vancouver, BC| V6H 3V9
> >
> > [de8e717f-8ef2-4754-96ce-a782e133b670]<
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> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
>
> ------------------------------
>
> Message: 11
> Date: Thu, 11 Mar 2021 21:30:46 +0530 (IST)
> From: "Abhik Ghosh Moulick" <abhik.ghosh.bose.res.in>
> Subject: [AMBER] constant ph md
> To: amber.ambermd.org
> Message-ID: <40300.103.230.166.2.1615478446.squirrel.bose.res.in>
> Content-Type: text/plain;charset=UTF-8
>
> Dear There,
> I am new in amber. I am trying to run constant ph molecular dynamics
> simulation in implicit solvent. I am following the tutorial given in amber
> website. I have some confusion. At first section 2 during heating of the
> system (http://ambermd.org/tutorials/advanced/tutorial18/files/heat.mdin)
> they are putting solvent ph to 7.5. I have not understood why they are
> heating the system with solvent ph 7.5. If I want to perform simulation in
> constant ph 1 or 2, is it necessary to keep solvent ph 7.5 during the
> heating step? Secondly at step 3 at first they do the equilibration at
> constant ph 4.5 and then perform simulation at various ph using output of
> the simulation run at ph 4.5. In my case, if I want simulation at ph 2
> then should I put ph value 2 at all the time?
> Thanks in advance.
> Best Regards
> ABhik
>
>
>
>
>
> ------------------------------
>
> Message: 12
> Date: Thu, 11 Mar 2021 11:16:40 -0500
> From: Adrian Roitberg <roitberg.ufl.edu>
> Subject: Re: [AMBER] constant ph md
> To: <amber.ambermd.org>
> Message-ID: <722a2414-2ccb-5a7d-a5b3-0cd58b85d0ad.ufl.edu>
> Content-Type: text/plain; charset="utf-8"; format=flowed
>
> Hi
>
> The tutorials, like all our tutorials, are not general recipes but
> rather a way to teach the techniques.
>
> In your case, if you are new to amber, I would suggest running some
> simpler simulations first to get your feet wet.
>
> As for your direct question:
>
> This is the input file in the tutorial:
>
> Implicit solvent constant pH initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=500, ntwx=500, nstlim=1000000,
> dt=0.002, ntt=3, tempi=100,
> temp0=300, tautp=2.0, ig=-1,
> ntp=0, ntc=2, ntf=2, cut=30,
> ntb=0, igb=2, tol=0.000001,
> nrespa=1, saltcon=0.1,*icnstph=1*,
> *solvph=7.5, ntcnstph=100000000*,
> gamma_ln=5.0, ntwr=500, ioutfm=1,
> nmropt=1, ntr=1, restraint_wt=2.0,
> restraintmask='.CA,C,O,N',
> /
> &wt
> TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,
> VALUE1=10.0, VALUE2=300.0,
> /
> &wt TYPE='END' /
>
> I put 3 variables in bold
>
>
> icnstph=1 means DO constant ph in implicit solvent
>
> solvph=7.5 means try a ph 7.5
>
> ntcnstph = 100000000 means try to change protonation states every those
> steps, which are set equal to 10 x nstlim.**This means that amber will
> never really try to change protoation states, and will stay at your
> initial setting for that.
>
> For the second question, the setting of 4.5 was an initial setup, so you
> can be ready to do other phs later on.
>
> If all you want if a single pH, by all means use that throughout.
>
>
> Adrian
>
> *
> *
>
> On 3/11/21 11:00 AM, Abhik Ghosh Moulick wrote:
> > [External Email]
> >
> > Dear There,
> > I am new in amber. I am trying to run constant ph molecular dynamics
> > simulation in implicit solvent. I am following the tutorial given in
> amber
> > website. I have some confusion. At first section 2 during heating of the
> > system (
> https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_advanced_tutorial18_files_heat.mdin&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=6m9itdHniQ3zNalYxdFWOb6qoOAOSuEW_VhkbqGjMrs&s=ZONzf_yihAw6wQy0N0oqOs6SgxRdEJz0NybZicTGX0Q&e=
> )
> > they are putting solvent ph to 7.5. I have not understood why they are
> > heating the system with solvent ph 7.5. If I want to perform simulation
> in
> > constant ph 1 or 2, is it necessary to keep solvent ph 7.5 during the
> > heating step? Secondly at step 3 at first they do the equilibration at
> > constant ph 4.5 and then perform simulation at various ph using output of
> > the simulation run at ph 4.5. In my case, if I want simulation at ph 2
> > then should I put ph value 2 at all the time?
> > Thanks in advance.
> > Best Regards
> > ABhik
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=6m9itdHniQ3zNalYxdFWOb6qoOAOSuEW_VhkbqGjMrs&s=U9q-IBxKUptQ1Nv_mkyXsbx0xnPgzcStoh8JodJw2mA&e=
>
> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
>
> ------------------------------
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>
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Received on Mon Mar 22 2021 - 08:30:02 PDT
