Re: [AMBER] NVT equilibriation followed by NPT in TI

From: David Case <>
Date: Tue, 17 Dec 2019 13:38:58 +0000

On Mon, Dec 16, 2019, Debarati DasGupta wrote:

>Page 327 Section 17.6.8 says it’s a good practice to do “NVT
>equilibration followed by NPT”…” Please note: in general you will need to
>equilibrate the temperature to something like the final temperature using
>constant volume (ntp=0) before switching on constant pressure simulations
>to adjust the system to the correct density”

>In my equilibration input files for my TI project, I have not followed
>this, is this possibly the reason why my system experiences high forces
>and GPU cannot handle the equilibration steps:

It's certainly a good idea to try. I'd also suggest doing a complete
"equilibration" at both end points (before turning on TI). Run for
quite a while on the GPU and see if any problems arise.

I'm sorry you are having so much trouble with this. I'm also guessing
taht most people on the list (like me) have lost track of all of the
things you have tried. The key to debugging is to try to find the
minimal change that goes from working to non-working. Two additional
general suggestions:

   don't set iwrap=1 (possible but unlikely culprit)
   use a restraint_wt of 10 rather than 100 (reduces large forces)

Since it's possible that there is problem with the ligand force field
parameters, try using something GLY in it's place, just to (again) try
to narrow down the possible causes of the problem.

...good luck...dac

AMBER mailing list
Received on Tue Dec 17 2019 - 06:00:02 PST
Custom Search