[gmx-users] initial velocities Langevin dynamics

[Ran Friedman]

Hi Loris,

It may be better to have ld_seed=-1. This way, you won't have the same
seed again when you restart.

@Article{Cerutti2008,
author = "Cerutti, D S and Duke, R and Freddolino, P L and Fan, H and
Lybrand, T P",
title = {Vulnerability in Popular Molecular Dynamics Packages Concerning
Langevin and Andersen Dynamics},
journal = "J Chem Theory Comput",
year = "2008",
volume = "4",
pages = "1669-1680"
}

Best regards,
Ran

Loris Moretti wrote:
> Dear Mark and Oscar, 
>
> Thanks for your help!
> I checked the velocity distribution and the velocity at different simulation frames. As you said the initial velocities are all set to zero and at the next step are already changed, I also guess by the random thermal noise.
>
> Thus, my idea of simulating the same system with different random generator number for thermal noise (ld_seed) might account for a small variation of the "initial" conditions? 
>
> loris...
>
>
> In message <8c3f24a40903110611j4f69c75emb0f5eef0484de783 at mail.gmail.com> Discussion list for GROMACS users <gmx-users at gromacs.org> writes:
>   
>>> Thus I am a bit confused about it!
>>>       
>>> I'm confused about the manual comment about only being meaningful with the
>>> MD integrator, but we 'll have to wait until someone who knows something
>>> about LD can post!
>>>       
>> For LD, the velocities will (should) get rescaled by the random thermal
>> noise, that is- by the Langivin thermostat.
>> With MD, the thermostat works like friction (positive or negative friction).
>> So you see, that for LD, an initial velocity of zero should next be changed
>> by the thermostat, while for MD the rescaling shouldn't work for zero.
>>
>> --Omer Markovitch.
>>
>> Koby Levy research group,
>> Weizmann Institute of Science.
>> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
>>     
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>   


-- 
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
------------------------------------------------------

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