Re: namd simulation​:protein,l​igand,lipi​d,water and ions

From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Jun 19 2012 - 12:37:13 CDT

Have you been able to successfully run a simulation with a different
system, such as one of the benchmarks on the NAMD site? I would first try
that, with the provided configuration files. If that works, then I would
use those coordinate and parameter files with your configuration. If that
still works, then it is likely you have something incorrect in your
coordinates/topology/parameters.

~Aron

On Tue, Jun 19, 2012 at 1:33 PM, Marlet Martinez <marletm8_at_gmail.com> wrote:

> Dear all,
>
> Thanks for your suggestions,
>
> I already installed the 2.8 namd version but I cant run my
> simulation, it stops again after message below comes (I already attached
> my .log file in the previous message). I am thinking maybe there is one
> problem in my simulation because no matter what version I use (2.6 or
> 2.8) my simulation stops automatically and coordinates are not even
> generated form the 02.conf
>
>
> -----------------------------
>
> Info: CREATING 1716 COMPUTE OBJECTS
>
> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
>
> Info: NONBONDED TABLE SIZE: 769 POINTS
>
> Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
>
> Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
>
> Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
>
> Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
>
> ---------------
>
> I would appreciate any suggestion,
>
> Thanks in advance,
>
> Mar,
>
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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