Re: [gmx-users] initial velocities Langevin dynamics
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 <8c3f24a40903110611j4f69c75emb0f5eef0484de...@mail.gmail.com>
> Discussion list for GROMACS users 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.fried...@bioc.unizh.ch
Skype: ran.friedman
--
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Re: [gmx-users] initial velocities Langevin dynamics
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 <8c3f24a40903110611j4f69c75emb0f5eef0484de...@mail.gmail.com> Discussion list for GROMACS users 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/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] initial velocities Langevin dynamics
> > 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/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] initial velocities Langevin dynamics
Loris Moretti wrote: Dear Mark, Thanks for answering! My question arises because in the manual is also reported that gen_vel "is only meaningful with integrator md" (mdp options section: velocity generation) Well it is much more effective to say that the first time. :-) Getting someone's attention to donate their time to you is more likely if you demonstrate that you've actively tried to find the answer. My reaction to your first post a week (or so) ago was to wonder why you hadn't looked in the manual. :-) This time, I actively pointed you at the manual, but now I find I didn't need to spend that time. This sort of thing can frustrate people who'd otherwise be happy to help. Do have a look at the link at the bottom of this page http://wiki.gromacs.org/index.php/Support and because I provide a .gro file with no velocities and I clearly specify in the .mdp not to generate velocity. If there's no source of velocities, then probably zero gets used for initial velocities. 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! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] initial velocities Langevin dynamics
Dear Mark, Thanks for answering! My question arises because in the manual is also reported that gen_vel "is only meaningful with integrator md" (mdp options section: velocity generation) and because I provide a .gro file with no velocities and I clearly specify in the .mdp not to generate velocity. Thus I am a bit confused about it! loris... In message <49b792a4.3070...@anu.edu.au> Discussion list for GROMACS users writes: > Loris Moretti wrote: > > Hello everybody, > > > > Sorry to post again the same question but I've got no answer so far. > > > > I have a technical question, it might be silly but I couldn't find an > > answer so far. How are assigned the initial velocities for the particles > > when Langevin dynamics is performed? > > > > In normal MD the gen_vel/gen_seed are used for random generation of the > > initial velocities. I am used to vary this number with the same system in > > order to explore the effect of different initial conditions. I was > > wondering if there is such a possibility with Langevin dynamics, like > > changing the ld_seed number? > > As you'll see in the manual (section 7.3.4) ld_seed is not used for > generating velocities. I expect gen_vel and gen_seed do this, since the > purpose of generating initial velocities doesn't change with the > integrator. You're still wanting to sample a Maxwell distribution, no? > > You could have experimented with gen_seed and used gmxcheck to compare > pairs of .tpr files to answer your own question. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] initial velocities Langevin dynamics
Loris Moretti wrote: Hello everybody, Sorry to post again the same question but I've got no answer so far. I have a technical question, it might be silly but I couldn't find an answer so far. How are assigned the initial velocities for the particles when Langevin dynamics is performed? In normal MD the gen_vel/gen_seed are used for random generation of the initial velocities. I am used to vary this number with the same system in order to explore the effect of different initial conditions. I was wondering if there is such a possibility with Langevin dynamics, like changing the ld_seed number? As you'll see in the manual (section 7.3.4) ld_seed is not used for generating velocities. I expect gen_vel and gen_seed do this, since the purpose of generating initial velocities doesn't change with the integrator. You're still wanting to sample a Maxwell distribution, no? You could have experimented with gen_seed and used gmxcheck to compare pairs of .tpr files to answer your own question. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] initial velocities Langevin dynamics
Hello everybody, Sorry to post again the same question but I've got no answer so far. I have a technical question, it might be silly but I couldn't find an answer so far. How are assigned the initial velocities for the particles when Langevin dynamics is performed? In normal MD the gen_vel/gen_seed are used for random generation of the initial velocities. I am used to vary this number with the same system in order to explore the effect of different initial conditions. I was wondering if there is such a possibility with Langevin dynamics, like changing the ld_seed number? thanks, loris... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] initial velocities Langevin dynamics
Hi there, I have a technical question, it might be silly but I couldn't find an answer so far. How are assigned the initial velocities for the particles when Langevin dynamics is performed? In normal MD the gen_vel/gen_seed are used for random generation of the initial velocities. I am used to vary this number with the same system in order to explore the effect of different initial conditions. I was wondering if there is such a possibility with Langevin dynamics, like changing the ld_seed number? thanks, loris... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
