Re: temperature-TS with NAMDplot

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jul 08 2011 - 08:09:57 CDT

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.

bjoern,

this doesn't solve the problem of bad energy conservation,
it merely hides it. a well set up MD simulation should conserve
energy for an extended period _without_ a thermostat. the use
of thermostat algorithms is (was) primarily meant to make a
small system behave like it was embedded in (and in equilibrium
with) a much larger environment for being able to correctly derive
observables from the simulation data. now, a _little_ drift is
unavoidable due to the truncation errors resulting from using
floating point numbers and a numerical integrator, and this
can be handled by the thermostat as well. but anything beyond
that turns your MD simulation from MD to something that is
more like a "guided MC" simulation.

there are many possible sources that will lead bad energy
conservation: too long a time step, very steep potentials,
high temperature, improper use of SHAKE (= rigidbonds)
or lack of it, bad multi-timestepping settings, bad choice
of PME grid and so on. each of these need to be investigated
for what causes the bad energy conservation and that needs
to be corrected. as noted before, this is easiest done by
running without a thermostat, after the system has been
properly equilibrated with it.

cheers,
     axel.

> 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
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.comhttp://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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