Re: Slow heating in namd

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Oct 15 2009 - 10:05:07 CDT

On Thu, 2009-10-15 at 10:10 -0400, Pavan G wrote:
> Hello All,
> I am trying to heat a protein in water in increments of 25k every 2ps. My
> config file is attached. The relevant part is the following:
>
> set temperature 325
> for {set i 100} {$i < $temperature } {incr i 25} {
> set tempr $i
> langevinTemp $tempr #temp to which langevin dynamics

try:
langevinTemp $tempr ; #temp to which langevin dynamics

you have to follow Tcl syntax.

cheers,
   axel.

> will be adjusted
> reinitvels $tempr
> run 2000
> }
>
> It runs fine for the first time and then dies with the error:
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
> OPENING COORDINATE DCD FILE
> WRITING COORDINATES TO DCD FILE AT STEP 1000
> WRITING COORDINATES TO RESTART FILE AT STEP 1000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 1000

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:34 CST