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, Aswathy Dept. Biotechnology Ext. 3108 ----- Original Message ----- From: "Mark Abraham" <[email protected]> To: "Discussion list for GROMACS users" <[email protected]> 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. Mark _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
md_final.mdp
Description: Binary data
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