[gmx-users] Water atoms cannot be settled

Ms. Aswathy S aswathys at amritapuri.amrita.edu
Wed Jul 8 15:44:46 CEST 2009

Thank you for your quick response. I am trying all these possibilities.

Can you please make me one thing clear, In certain   papers and tutorials it is seen that , for production run they are using either NPT or NVT. Which one should i try for my protein ligand complex.(Right now I did NVT condition) attaching the mdp file.

Thanks & Regards,
Dept. Biotechnology
Ext. 3108

----- Original Message -----
From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, July 8, 2009 5:27:42 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: Re: [gmx-users] Water atoms cannot be settled

Ms. Aswathy S wrote:
> Hi ,
> I am doing a protein ligand Md simulation.
> 1. I did the energy minimization
> 2. A 500 ps NVT equilibration
> 3. then a 1 ns NPT simulation , and seemed that the system is equilibrated enough I went ahead with Md run for 5 ns.
> But at the step of 70000 I got the error like "Some of the water atoms cannot be settled." I understood that some water molecules making bas contacts/ or clashes. But How can I rectify that ? Do I need to continue with equilibration again? or any tother way to get out of this problem"?
> Attaching the equilibration parameter files here with .
> Please tell me your comments, Thanks

You can try removing your position restraints before you change the 
ensemble to NPT. Also you should inspect the trajectory visually to see 
whether you can deduce what the problem is from its symptoms. Further, 
look to see how much your box size is changing when you switch to NPT. 
You'd prefer it didn't change a great deal - and if it does, 
equilibrating longer is likely to be needed.

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