Re: temperature-TS with NAMDplot

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Fri Jul 08 2011 - 07:23:44 CDT

Or use the Lowe-Andersen thermostat instead of the Langevin thermostat:
loweAndersen on
loweAndersenTemp 300.0

Cheers,
Johan

------------------------------------------------------------------------------------------------------
Johan Strumpfer:         johanstr_at_ks.uiuc.edu        www.ks.uiuc.edu/~johanstr
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
------------------------------------------------------------------------------------------------------

On Fri, Jul 8, 2011 at 7:30 AM, Bjoern Olausson <namdlist_at_googlemail.com> wrote:
> 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-Universität Halle-Wittenberg
> Fachbereich Biochemie/Biotechnologie
> Kurt-Mothes-Str. 3
> 06120 Halle/Saale
>
> Phone: +49-345-55-24942
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:27 CST