[gmx-users] Energy minimization of crystal structure with water

NG HUI WEN HuiWen.Ng at nottingham.edu.my
Mon Mar 19 03:43:19 CET 2012

Hi Mark,

Thanks - I completely forgot about that!


From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Sunday, March 18, 2012 2:03 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy minimization of crystal structure with water

On 18/03/2012 1:01 PM, NG HUI WEN wrote:

Hi all,

I have a seemingly simple task that turned quite tricky here.

I am trying to perform energy minimization on a crystal structure after adding hydrogen to the protein using pdb2gmx (OPLS).

The problem I am facing now is that after energy minimization, the protein and water (originally in the protein cavity) were found in completely different coordinate space. Using "pbc box" in VMD, I found that the water was found roughly at the original space but not the protein.

I have tried (all turned out futile)

1) EM with and without pbc

2) position restraint the protein backbone and water

Would someone be able to help me on this? I know I must have done something silly here.

This is normal. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

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