From: B.W.J. Irwin (bwji2_at_cam.ac.uk)
Date: Fri Dec 02 2016 - 04:43:49 CST
If the density of the system is a bit off, I have found one may need to
restart a couple of times with NPT,
if the box rescales too quickly some of the grids set up for the
original volume exceed some threshold and the program crashes.
Assuming the NPT runs for a while before crashing (if it crashes
immediately it might be another problem)
Remedy,
Run NVT
Run NPT from NVT coords saving restarts at an appropriate frequency
Run short NPT from restart coords
Run short NPT from restart coords
Run short NPT from restart coords
repeating until the error stops
Run long NPT
You should be able to verify if this was the problem by tracking the
volume of the system as you make the transition from NVT to NPT
Hope this helps,
Ben
On 2016-12-01 21:21, faride badalkhani wrote:
> Dear NAMD users,
>
> I am performing MD simulations on a polymer in water. I performed
> 20000 steps of minimization (time step : 1 fs) and then 2 ns of NVT
> simulations without any problem. Then I wanted to change the ensemble
> to NPT, but I got the following error:
> Low global exclusion count errors!
>
> I wonder if the system is unstable because it has been running without
> getting error for 2 ns before going to NPT simulation.
>
> P.S. The structure includes an alkyne group that I got its parameters
> from CHARMM GENERAL force field, but there is no dihedral types in
> CGen FF for it.
>
> Regards,
> Farideh
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