[gmx-users] compressing the system

Moeed lecielll at googlemail.com
Mon Aug 2 21:25:36 CEST 2010

Dear Dr. Chaban and Justin,

Actually I am exactly using the same settings Dr. Chaban suggested because I
know you are the experts in the field and what Dr. Chaban suggested was
indeed the only way of compressing my 8 chain-system to the density I want.
Before that I tried more than 30 NPT (with berendsen) and NVT simulations in
one week to get a more realistic shape of the chain but they never worked
(crash) when box becomes small. When you experts suggest sth I follow that
for sure (especially since unfortunately I am the only person in the group
dealing with molecular simulations and the archive and literature are my
only advisors! I myself had no background on MD either when I started...). I
appreciate your help.

(The only issue I had was unsimilar energy values (KJ/mol).. I just changed
PME to shift because at the moment I am not doing simulation on our cluster
and PME runs take weeks to finish on my local machine. so after I used the
exact settings (with PME) as you suggested I will get back to you about
energy values).

The density of around 800 (SI) is just fine and I am not trying to make the
system smaller at all. The issue at this time is that surprisingly, when I
use the same mdp file for *only one single* chain simulation crashes and I
get the error message that CUTOFF is less than LBOX/. You (Dr.Chaban)
suggested 30 bar pressure for 8 chains. Given the error I got I reduced
pressure to even 1 bar. with this pressure I am not the getting the cutoff
error but simulations crash ... The same problem I had before. ..
(I also altered tau_p in the range of 0.5 to 10 and tried different
combinations of tau_p and ref _p but didnt succeed)

Could you please give me comments on appropraite P coupling settings?

I have also a very important question: I read yesterday somewhere in the
archive of the year 2007 about validity of the forcefiled at low pressures
(~1 bar). I am planning to do simulations at very high pressure (200bar) and
400K to calculate surface tension and solubility paramater of PE-haxane
polymer solution. Is there any way of using ff parameters (which are
calculated for low pressure) at higher pressures?

Moeed :)
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