Re: temperature-TS with NAMDplot

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Fri Jul 08 2011 - 06:30:09 CDT

On Friday 08 July 2011 12:44:50 Molecular Dynamics wrote:
> Dear Namd users,
>
> I have run a 30 ns md simulation at 300 K in NVT using langevin method.
> After the simulation I made a plot for temperature-TS with NAMDplot in
> VMD. But I saw that temperature was fixed above 300 K . What is the reason
> for this ?
> Please examine the graph of temperature-TS and the main parts of conf file
> from the link below
> http://uploading.com/files/38719fc4/namd_temp-ts.rar/
>

Looks like the mean is of by ~10 K. Looks pretty much to me.
For my simulations the mean is pretty close to the set temperature.

For example:
Target: 303K
MIN: 199.2046 @1100
Max: 304.8586 @332100
MEAN: 302.27269461
STD: 2.4002367513

To counteract your Problem I would suggest to increase the friction (Langevin
damping coefficient) to something around 5/ps or at least 2/ps instead of
1/ps.

You might want to make yourself a bit more familiar what the "Langevin damping
coefficient" does before choosing a value.

Kind regards,
Bjoern

-- 
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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