Hi Batuhan,
What you report is correct and expected - although we should probably modify the output not to report the pressure here.
The pressure comes from the virial but when one uses a Monte Carlo Barostat there is no virial in the expression - as such the code does not calculate it and the reported pressure is thus zero. The virial is an expensive calculation in parallel requiring all to all communication and reductions. Since it is only cosmetic when running with a Monte Carlo Barostat one would just be wasting time here. Sander, isn't so aggressive with the optimizations and thus still calculates the virial and reports the pressure even though it doesn't actually do anything with that value.
In reality the pressure is not of great use in determining if your simulation is stable or converged since it fluctuates wildly. It's probably better just to look at the density as a function of time and this is reported.
Hope that helps.
All the best
Ross
> On Feb 5, 2016, at 8:10 AM, Batuhan Kav <bkav13.ku.edu.tr> wrote:
>
> Dear All,
>
> I have a system of two trisaccharides in explicit water box. I run my simulations in NPT with pmemd.cuda, however info files always output to zero pressure. I use MC barostat for pressure control.
>
> I run minimization, heating and a short equilibration runs with sander, then I proceed to use pmemd.cuda for the production runs. Until I switch to cuda implementation, info files output nonzero pressure values, however with cuda I always get pressure=0, as below.
>
> NSTEP = 900000 TIME(PS) = 2050.000 TEMP(K) = 300.67 PRESS = 0.0
> Etot = -39710.3760 EKtot = 7873.7148 EPtot = -47584.0908
> BOND = 51.7412 ANGLE = 78.5973 DIHED = 7.8085
> 1-4 NB = 43.2666 1-4 EEL = 1162.9210 VDWAALS = 8634.6618
> EELEC = -57563.0872 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 131390.9400
> Density = 0.9999
>
> For instance, while using sander for initial equilibration run, I get (however negative)
>
> NSTEP = 100000 TIME(PS) = 250.000 TEMP(K) = 297.05 PRESS = -17.2
> Etot = -39803.0263 EKtot = 7779.0082 EPtot = -47582.0344
> BOND = 47.0929 ANGLE = 79.1150 DIHED = 5.0144
> 1-4 NB = 45.7862 1-4 EEL = 1159.6999 VDWAALS = 8796.6486
> EELEC = -57715.3915 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 3838.4464 VIRIAL = 3887.1530 VOLUME = 131307.0964
> Density = 1.0005
>
> I checked my input files couple of times and couldn’t catch an error/mistake. I just wanted to ask if these nonzero pressures values are normal (which I don’t think). Also, what might be the reason that I am getting zero pressure with cuda implementation? I attach my input files. 03_Prod_ini.in is the input file for short equilibration with sander, and 03_Prod.in is the actual production run input.<01_Min.in><02_Heat.in><03_Prod_ini.in><03_Prod.in>
>
> Thank you,
> Batuhan_______________________________________________
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Received on Fri Feb 05 2016 - 09:30:02 PST
