Dear mr. Simmerling,
Thank you very much for the help.
I was able to solve the problem by running the few first initial steps on CPU and then going back to GPU.
The system is running fine now. I don't understand how this affects the simulation, but what matters is that, from the first production frames I've looked into, the system is behaving well. Thank you 🙂
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Sunday, April 10, 2022 16:54
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Barostat not working (?)
I'd suggest looking at your starting structure and force field. Was any of
the structure modeled, or built in a way that might be unstable? Did you
use any non standard force field? These are the most common causes for this
behavior. You can also try setting ntpr to a smaller number so you can get
more details about how the energy is changing that leads to the problem. At
this point it's hard to debug from the outside, since the error message is
telling you that your system is not behaving well. You're in the best
position to know why that might be the case.
On Sun, Apr 10, 2022, 11:26 AM Artur Hermano <artur.hermano.hotmail.com>
wrote:
> Dear mr. Simmerling,
>
> thank you for your advice. Indeed, the output file from my queueing system
> tells me this:
>
> "ERROR: Calculation halted. Periodic box dimensions have changed too much
> from their initial values.
> Your system density has likely changed by a large amount, probably from
> starting the simulation from a structure a long way from equilibrium.
>
> [Although this error can also occur if the simulation has blown up for
> some reason]
>
> The GPU code does not automatically reorganize grid cells and thus you
> will need to restart the calculation from the previous restart file.
> This will generate new grid cells and allow the calculation to continue.
> It may be necessary to repeat this restarting multiple times if your
> system
> is a long way from an equilibrated density."
>
> It still doesn't make sense because my system density has been stable up
> until the halting occurs... I've tried adding restraints and increasing
> both minimization and NVT heating simulation times, but it was no use...
> Would you have any suggestions as of what I could do instead of run
> multiple restarting runs?
>
> Thank you!
>
> Artur
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, April 8, 2022 18:27
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Barostat not working (?)
>
> the pressure will fluctuate (it's not constant in an instantaneous sense),
> but your density looks good so I think it's ok.
>
> I don't think that's related to why it stops. did you get any error message
> to another file, maybe something output from your queueing system?
>
> On Fri, Apr 8, 2022 at 4:47 PM Artur Hermano <artur.hermano.hotmail.com>
> wrote:
>
> > Hello Amber team,
> >
> > I am trying to run a simulation that, after minimization goes through a
> > NVT heating step and then through a NPT equilibration step. I am using
> the
> > Berendsen barostat for the NPT step, but it seems not to be working.
> > Despite the previous steps running fine, my equilibration stops all of a
> > sudden with no error messages on the bottom of the equi.out file (see
> > below). My equilibration input file is:
> >
> > Equi
> > &cntrl
> > imin=0,
> > ntx=5,
> > irest=1,
> > nstlim=50000,
> > dt=0.002,
> > ntf=2,
> > ntc=2,
> > tempi=300.0,
> > temp0=300.0,
> > ntpr=500,
> > ntwx=500,
> > cut=10.0,
> > ntb=2,
> > pres0=1.0,
> > ntp=1,
> > taup=2.0,
> > ntt=3,
> > gamma_ln=1.0,
> > /
> >
> > And these are the bottom lines of my equi.out file:
> >
> > NSTEP = 22500 TIME(PS) = 145.000 TEMP(K) = 300.69 PRESS =
> > -80.5
> > Etot = -106653.7224 EKtot = 27528.5859 EPtot =
> > -134182.3083
> > BOND = 1203.8180 ANGLE = 3190.8939 DIHED =
> > 5012.8786
> > 1-4 NB = 1420.7867 1-4 EEL = 13569.6107 VDWAALS =
> > 14268.7934
> > EELEC = -172849.0895 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 11546.7037 VIRIAL = 12320.0722 VOLUME =
> > 444926.8592
> > Density =
> > 1.0244
> >
> >
> ------------------------------------------------------------------------------
> >
> >
> > NSTEP = 23000 TIME(PS) = 146.000 TEMP(K) = 298.83 PRESS =
> > 16.8
> > Etot = -106989.9082 EKtot = 27357.8926 EPtot =
> > -134347.8008
> > BOND = 1195.2600 ANGLE = 3169.3732 DIHED =
> > 5000.9721
> > 1-4 NB = 1405.4871 1-4 EEL = 13560.7227 VDWAALS =
> > 14215.4113
> > EELEC = -172895.0271 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 11520.0326 VIRIAL = 11358.4814 VOLUME =
> > 444598.2344
> > Density =
> > 1.0251
> >
> >
> ------------------------------------------------------------------------------
> >
> >
> > NSTEP = 23500 TIME(PS) = 147.000 TEMP(K) = 296.37 PRESS =
> > -3.2
> > Etot = -107084.2024 EKtot = 27133.1016 EPtot =
> > -134217.3040
> > BOND = 1180.1769 ANGLE = 3129.3570 DIHED =
> > 5012.9329
> > 1-4 NB = 1429.4178 1-4 EEL = 13670.0174 VDWAALS =
> > 14530.8318
> > EELEC = -173170.0378 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 11581.9544 VIRIAL = 11612.9675 VOLUME =
> > 444105.4865
> > Density =
> > 1.0263
> >
> >
> ------------------------------------------------------------------------------
> >
> >
> > NSTEP = 24000 TIME(PS) = 148.000 TEMP(K) = 300.35 PRESS =
> > -32.2
> > Etot = -107062.9372 EKtot = 27496.6387 EPtot =
> > -134559.5759
> > BOND = 1142.9891 ANGLE = 3215.9534 DIHED =
> > 4999.4223
> > 1-4 NB = 1424.9494 1-4 EEL = 13680.1911 VDWAALS =
> > 14481.5016
> > EELEC = -173504.5828 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 11601.6809 VIRIAL = 11910.2262 VOLUME =
> > 444245.4810
> > Density =
> > 1.0260
> >
> >
> ------------------------------------------------------------------------------
> >
> >
> > NSTEP = 24500 TIME(PS) = 149.000 TEMP(K) = 297.84 PRESS =
> > -72.4
> > Etot = -107278.1062 EKtot = 27267.2070 EPtot =
> > -134545.3133
> > BOND = 1135.5286 ANGLE = 3195.0653 DIHED =
> > 5006.3317
> > 1-4 NB = 1414.9647 1-4 EEL = 13662.5592 VDWAALS =
> > 14327.2018
> > EELEC = -173286.9645 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 11442.0238 VIRIAL = 12135.9224 VOLUME =
> > 443834.8519
> > Density =
> > 1.0269
> >
> >
> ------------------------------------------------------------------------------
> >
> > As you can see, the pressure is clearly far from constant, but I don't
> > think it should... Am I missing something here? Any help is very much
> > appreciated!
> >
> > Thank you so much in advance!
> >
> > Artur
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sun Apr 10 2022 - 13:30:03 PDT
