Re: Slow heating in namd

From: Pavan G (pavan.namd_at_gmail.com)
Date: Thu Oct 15 2009 - 10:37:47 CDT

Thanks a bunch for your input Roman.
Axel, Tcl/Tk was the cause of the problem. Thanks for you time.
Pavan

On Thu, Oct 15, 2009 at 11:32 AM, Roman Petrenko <rpetrenko_at_gmail.com>wrote:

> there is one trick which once worked for me:
>
> run many minimization steps (like 10,000). the system will be cooled
> down so much that it takes much longer to heat it up, and
> correspondingly you avoid fast movement of atoms which usually causes
> namd to quit.
>
> another comment is look at the energy output, it will be high if you
> have at least 2 atoms overlapping in space.
>
> and finally, increase output report (say, output every step or every
> 10nth step), then you'll know exactly at which point in trajectory the
> system broke down.
>
> On Thu, Oct 15, 2009 at 10:10 AM, Pavan G <pavan.namd_at_gmail.com> 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
> > 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
>
>
>
> --
> Roman Petrenko
> Physics Department
> University of Cincinnati
>

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