Re: Error while running NPT Simulation

From: Audrey Salazar (alsalazar_at_u.northwestern.edu)
Date: Thu Oct 16 2008 - 13:51:30 CDT

Hello
There are quite a few posts on this. Have you pasted your error message to
search the NAMD-L archive?

Audrey

On 10/16/08, Nd S <navdeep79_at_gmail.com> wrote:
>
> Hi all
>
> I ran a NPT simulation and the volume of the cell decreased from
> 1,001,290.4628 to 471,602.1941 and after that the simulation crashed giving
> the following error:
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 65000
> WRITING COORDINATES TO DCD FILE AT STEP 65000
> WRITING COORDINATES TO RESTART FILE AT STEP 65000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 65000
> FINISHED WRITING RESTART VELOCITIES
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> I ran the simulation for 100,000 steps. The unit cells contains only a
> derivative of 1-Hexene. Can you please explain me what happened and how I
> can correct this.
>
> Thanks a lot,
> Navdeep
>

-- 
Audrey L. Salazar
Amaral Research Group
Dept. of Chemical and Biological Engineering
Northwestern University
Evanston, IL USA
Phone: 847.491.2188

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