Re: regarding simulation

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue May 05 2009 - 10:16:04 CDT

It's probably because you're using a very short cutoff, no long range
electrostatics, and a high dielectric with a (presumably) solvated system.
Peter

prasun kumar wrote:
> respected all
>
> I have just now started simulation using NAMD
> for MD I am using *numsteps *parameter in place of *minimize* that i
> have used while doing minimization. till minimization its working fine.
> actually I want to check the interaction between two proteins for that I
> need to do the simulation. Now the problem I am facing is following:
>
> Energy of the system is increasing continuosly and the volume is also
> increasing.
> I am attaching my configuration file also.
> The problem I am facing is it because of the fact that I m not using NVT
> during my simulation or some thing else. I am getting the same result
> when I am replacing *numsteps *by *run*.
>
> lookin forward for your positive reply
>
> with regards
>
> PRASUN (ASHOKA)
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:53 CST