Re: namd2 still works but without any new messages in log file

From: Bjoern Olausson (
Date: Thu Jul 01 2010 - 09:27:47 CDT

On Thursday 01 July 2010 14:21:18 wrote:
> Dear everyone:
> I am doing molecular dynamics simulation using NAMD2.7b2. There are some
> weird thing happened in my minimization. I set 1000 steps for
> minimization, however, NAMD stops at step 551. It seems still working
> because the CPU utilization is still 100%. But there is no any new data or
> error report being written in my log file. Then I restart the minimization
> from the beginning, the same thing happens. Can anyone give some
> suggestions? I would highly appreciate for your help! Many thank!
> Sincerely
> Xubin Li
> Lanzhou University
> China

Hi Xubin,

what I will suggest does not explain what is happening, but it sounds like a
problem I came across some time in the past and when I remember correctly
there was someone else asking this question on the mailinglist an he got the
same answer from me.

My solution was to minimize my structure using the very simple and robust line
minimizer from CHARMM. After that I was able to minimize the structure with
NAMD or run the simulation at once.

What also worked was a older version of NAMD (2.6) which minimized my system
without trouble. After that I could continue with 2.7

Looks like the minimizer in 2.7 is a bit more picky then it was in 2.6.

I didn't investigate in this further but you might also overcome your problem
by adjusting the "minTinyStep" or "minBabyStep" steps for the minimizer.

Still it is unclear why NAMD keeps running in the background but no longer
yielding data.

Maybe anyone with more in detail knowledge about the NAMD 1.6 vs. 1.7
minimizer can comment on this.

Kind regards

Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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