[gmx-users] box of simulation

mohammad agha mra_bu at yahoo.com
Tue Aug 14 14:51:28 CEST 2012

Dear Mark,

Thank you very much from your help.

Best Regards

----- Original Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, August 14, 2012 2:44 PM
Subject: Re: [gmx-users] box of simulation

On 14/08/2012 6:55 PM, mohammad agha wrote:
> Dear Mark,
> Thank you very much from your help.
> I used from genbox to place solvent molecules. my question is : In the NPT ensemble, for equilibrium, may the box become smaller than definite sizes before equilibrium(for example 2nm become smaller)

Yes, but that would normally indicate you should go back and fix some problem.

>   and if yes, why haven't been placed molecules in the box smaller before equilibrium initially and they need to more size and during equilibrium become smaller?

Depends. Maybe you changed the box size after generating solvent. Maybe you've mismatched your files. Maybe you ordered genbox not to fill the box with -maxsol. Maybe you didn't use a valid solvent box with genbox -cs. Maybe your model physics is broken somehow (like missing parameters, or inappropriate pressure coupling algorithm). Maybe you didn't read your output for warnings and information well enough. There's probably other causes too.

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