[gmx-users] Load imbalance and Y size error

nikhil damle pdnikhil at yahoo.co.in
Thu Oct 8 10:40:04 CEST 2009

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 ?


From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at 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.

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