No. My system is a single protein with charged ligand associated with it. But
why should box size shrink ? In solvated system it does not shrink. What effect
vacuum could possibly have on it ?
Regards,
Nikhil
________________________________
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Thu, 8 October, 2009 12:46:56 PM
Subject: Re: [gmx-users] Load imbalance and Y size error
nikhil damle wrote:
> Hi,
>
> I tried to run on single node now. Now the error is different saying
> "One of the box vectors has become shorter than twice the cut-off length or
> box_yy-|box_zy| or box_zz has become smaller than the cut-off"
>
> This means that my box shrinks during dynamics (this is not constant volume
> MD) But when Solvent is present in the same system, this does not happen. How
> should i deal with it then ?
If it's not constant volume then the simulation will change volume. Why should
your charged proteins want to stay at the original distance from each other? It
seems they want to collapse onto each other. You need to rethink your choice of
ensemble.
Mark
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