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.
Thank you,
Batuhan
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- application/octet-stream attachment: 01_Min.in
Received on Fri Feb 05 2016 - 08:30:03 PST
