[gmx-users] Dubious results with NPT

sujith ks sujithks58 at gmail.com
Mon Feb 24 05:37:08 CET 2014


  Thank you both for  the comments. I am using gromos96 forcefield . I read
a little bit  and as you said the nonbonded cutoff has to be higher.
The tau_p=5ps was chosen , since the manual mentions that the value has to
be raised by 4-5 times on going from berendsen to parrinello-rahman
barostat, though I did not completely follow the reasons behind it. I will
try with lower values.

   I had run an earlier simulation with the same parameters for a pure water
system for 5ns and reference pressure 5bar, and things worked fine there
with the average pressure at 5.15bar. I guess the sigma  for the case of
water was low and therefore the small cut-off of 0.8nm did not matter.
However the case of cyclohexane alone remains to be tried.

I guess Dr Vitaly was saying about using a switch/shift function.
I will try the simulation with the new settings and see.




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