[gmx-users] Re: NPT MD Run Problem

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 11 22:27:40 CET 2010

teklebrh at ualberta.ca wrote:
> Dear Justin.
> I turned off the gen-vel to no. Yes you are right. But I got the same 
> error.
> I increase tau-p ( from 1 to 3) and it looks working fine so far.
> One of the warnings is that the pressure is less 1%.

It could be that your previous equilibration was a bit insufficient to relax 
whatever the system is so there are still some colliding particles that cause 
the temperature to spike.  Increasing tau_p makes the coupling a bit weaker, 
allowing for some greater fluctuation, but you still may run into problems.

> Thank you for your help Justine.
> ================================
> Remark from the previous request
> The pdb2gmx is also working .... the reinstalled the .rtp file and it is 
> ok!
> I got the Toluene topology from the PHE.
> ===================================
> I want the same for the n-heptane toplogy using the pdb2gmx.... is there 
> any method I could get that from the gromos96 force filed. Just to avoid 
> using PRODRG!

To use pdb2gmx, you need an .rtp entry.  For something like united-atom 
n-heptane, this should be a relatively easy exercise, even to write the topology 
by hand.  See the manual.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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