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
