Re: Slow heating in namd

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Thu Oct 15 2009 - 10:32:43 CDT

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

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