Re: Error while running NPT Simulation

From: Audrey Salazar (alsalazar_at_u.northwestern.edu)
Date: Thu Oct 16 2008 - 13:55:55 CDT

Explanation of what happened (I think that this could be clarified
slightly):
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2057.html (look at
whole thread to get gist. Hrant's comment is most beneficial)

Audrey

On 10/16/08, Audrey Salazar <alsalazar_at_u.northwestern.edu> wrote:
>
> 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

-- 
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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