[gmx-users] Freeze groups and pressure

[Anton Feenstra]

Satyan Sharma wrote:
> 
> Hi all,
> I tried to simulate a dipeptide in water. A shell of 1
> nm was made around the peptide and everything outside
> the shell was frozen. The press coupling was set to no
> and the ref_t was zero for the frozen group.Now after
> 1ns of simulation I am getting a major drift in LJ(SR)
> which increases the pot. energy of system. The
> g_energy analysis showsa an output something like this
> :
>                Tot-Drift
> LJ (SR)          5300.33
> 
> Potential       5314.29
> 
> Could somebody explain this to me and where the
> problem could be...

You are simulating a very peculiar system indeed. If I understand
you correctly, you have in essence an ice-cube with a spherical liquid
'hole' in the middle, where your protein sits. I have no experience
with this type of set-ups (and would be hard pressed to see its 
implications and its possible use), but it doesn't seem strange to
me that the system undergoes extensive adaptations, which might well
include (large) energy drifts of any kind...

I'm afraid this isn't very helpful, but it might spark other
reactions...

-- 
Groetjes,

Anton
 ________ __________________________________________________________
|        | Anton Feenstra                                           |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam   |
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