[gmx-users] Load imbalance and Y size error

Berk Hess gmx3 at hotmail.com
Thu Oct 8 11:48:31 CEST 2009


Do not "randomly" change the fourierspacing.
Are you really using PME in vacuum?

The box size can only change if you have pressure coupling turned on,
which should, obviously, should not do in vacuum.


Date: Thu, 8 Oct 2009 15:13:25 +0530
From: pdnikhil at yahoo.co.in
Subject: Re: [gmx-users] Load imbalance and Y size error
To: gmx-users at gromacs.org

Now when i increased the fourierspacing from 0.12 to 0.22 nm, it worked properly on single node and failed on multiple nodes giving same error of
"The Y-size of the box (4.612312) times the triclinic skew factor (0.866052) is smaller than the number of DD cells (2) times the smallest allowed cell size(2.000000)"

What possibly could be the reason ? 


From: nikhil damle <pdnikhil at yahoo.co.in>
To: Discussion list for GROMACS users
 <gmx-users at gromacs.org>
Sent: Thu, 8 October, 2009 2:10:04 PM
Subject: Re: [gmx-users] Load imbalance and Y size error

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>
 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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