[gmx-users] Re: gmx-users Digest, Vol 61, Issue 29
Jacek Czub
jczub at gwdg.de
Fri May 8 11:58:25 CEST 2009
Ania, ja nie wzialem laptopa dla Ciebie :-( wezmiesz go ? :-*
gmx-users-request at gromacs.org wrote:
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. x2top and OPLS-AA vs. fudged 1-4 interactions (Vasilii Artyukhov)
> 2. Re: v-rescale - harmonic oscillator (servaas)
> 3. RE: Re: v-rescale - harmonic oscillator (Berk Hess)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 8 May 2009 13:07:02 +0400
> From: Vasilii Artyukhov <darth.vasya at gmail.com>
> Subject: [gmx-users] x2top and OPLS-AA vs. fudged 1-4 interactions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <91220afc0905080207vc411cf5of28da3eddb73efb4 at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear colleagues,
>
> I'm looking for clarifications on what exactly I need to do in order to get
> a correct scaling of 1-4 interactions for OPLS-AA in a topology made by
> x2top. Specifically, will the command
>
> x2top -f in.gro -o out.top
>
> result in a topology that, when fed into grompp, will give a .tpr that is
> correct in this respect? Or should I use the same command with the -nopairs
> option and let grompp generate the pairs basing on the [ defaults ] section
> of ffoplsaa.itp? Or did I miss the correct way to use x2top altogether
> (nexcl=4? something with dihedrals? etc.)?
>
> I'm trying to check if OPLS parameters are suitable for the description of a
> somewhat unusual system, and so far, the geometry of the system seems to get
> distorted by some intramolecular nonbonded interactions; I'd like to know
> whether that's because of unsuitable FF parameters, a bad topology, or both
> :)
>
> The version of GROMACS is presently 3.3.3, but I'm actually going to use
> 4.x. for this once I know how to use x2top properly.
>
> Thanks in advance,
> Vasilii
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090508/8b339ca0/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Fri, 08 May 2009 11:17:33 +0200
> From: servaas <servaas.michielssens at student.kuleuven.be>
> Subject: [gmx-users] Re: v-rescale - harmonic oscillator
> To: gmx-users at gromacs.org
> Message-ID: <1241774253.6575.2.camel at servaas>
> Content-Type: text/plain
>
> Hi,
>
> Thanks for your confirmation of this problem. One thing is not clear to
> me from your answer. Has v-rescale fundamental problems with a Harmonic
> oscillator or is it a problem with the GROMACS implementation?
>
>
> Kind regards,
>
> Servaas
>
>
>
>> Message: 3
>> Date: Fri, 8 May 2009 10:12:45 +0200
>> From: Berk Hess <gmx3 at hotmail.com>
>> Subject: RE: [gmx-users] Re: v-rescale - harmonic oscillator
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <COL113-W10F68330EA113929CBC3518E640 at phx.gbl>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>> Hi,
>>
>> I have come to the conclusion that the v-rescale thermostat is only correct
>> in the limit of large numbers of degrees of freedom, which is equivalent to a small scaling limit.
>> The conservation of the conserved energy quantity improves as the system gets bigger.
>>
>> But I noticed that in 4.0 the energy conservation is not good.
>> It can be improved significantly by changing line 164 or src/mdlib/update.c from
>> vv = lg*(vn + f[n][d]*w_dt);
>> to
>> vv = lg*vn + f[n][d]*w_dt;
>>
>> There are some other similar lines in case you are PR p-coupling or cosine acceleration.
>>
>> I will probably not fix this for 4.0.5, but only for 4.1, so we do not change
>> the reproducibility in minor revisions.
>>
>> Berk
>>
>>
>>
>>> From: servaas.michielssens at student.kuleuven.be
>>> To: gmx-users at gromacs.org
>>> Date: Thu, 7 May 2009 15:27:37 +0200
>>> Subject: [gmx-users] Re: v-rescale - harmonic oscillator
>>>
>>> Hi Berk,
>>>
>>> Thank you for your concern on this issue. It did not expect it to be a
>>> problem from the paper of Bussi et al., but it is of course possible.
>>> I am very curious to hear what they have to say about this. Are you
>>> contacting him or will I do it?
>>>
>>> For the rotational degrees of freedom would removing them with
>>> comm_mode=angular be a problem then because you are using restraints?
>>> (you use orire than?)
>>>
>>> Thanks again,
>>>
>>> Servaas
>>>
>>>
>>>> Hi,
>>>>
>>>> With a diatomic molecule there is the issue that the rotation of the molecule has two degrees of freedom
>>>> which are completely uncoupled from the rest of the system.
>>>>
>>>> Anyhow, I made a 1D harmonic oscillator using a position restraint and even there the energy
>>>> does not seem to be conserved.
>>>> I am not sure if a harmonic oscillator is a pathetic case, like with Nose-Hoover,
>>>> or if this is an issue with the integrator implementation in Gromacs.
>>>> I might need to ask Bussi about this.
>>>>
>>>> Berk
>>>>
>>>>
>>>>> From: servaas.michielssens at student.kuleuven.be
>>>>> To: gmx-users at gromacs.org
>>>>> Date: Thu, 7 May 2009 14:03:30 +0200
>>>>> Subject: [gmx-users] v-rescale - harmonic oscillator
>>>>>
>>>>> Hi,
>>>>>
>>>>> It is just a diatomic molecule without other interactions (so only
>>>>> bonded interaction, LJ=0 and charges=0 on the atoms). What other details
>>>>> would you like to know? Should I send you the tpr file?
>>>>>
>>>>> Servaas
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> No, only for small values is should be off, maybe tau_t < 10 or 100 * delta_t.
>>>>>>
>>>>>> How did you set up your harmonic oscillator?
>>>>>>
>>>>>> Berk
>>>>>>
>>>>>>
>>>>>>> From: servaas.michielssens at student.kuleuven.be
>>>>>>> To: gmx-users at gromacs.org
>>>>>>> Date: Thu, 7 May 2009 12:54:54 +0200
>>>>>>> Subject: [gmx-users] Re: v-rescale - harmonic oscillator
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Thank you for your reply.
>>>>>>>
>>>>>>> Yes by effective energy I mean the Gromacs conserved energy term.
>>>>>>>
>>>>>>> So you would say the cause of my problem here is that I need a small
>>>>>>> tau_t to thermostat this system but for small tau_t values the algorithm
>>>>>>> is not 100% ok yet? And what are very small tau_t values? I tested with
>>>>>>> quite a big range here.
>>>>>>>
>>>>>>> The problem occurred to me when I was experimenting with a hybrid monte
>>>>>>> carlo algorithm. I first tested it on a noble gas and compared to MD
>>>>>>> simulation with nose-hoover and v-rescale. Those results were 100%
>>>>>>> identical. Then I tried it on a dipeptide in vacuum, results were a
>>>>>>> little off here (I would expect this for nose-hoover thermostat, but not
>>>>>>> for v-rescale). So I decided to go the the extreme simple case of a
>>>>>>> harmonic oscillator. Those results were seriously off, and then I
>>>>>>> checked the conserved energy term, which seems impossible to keep it
>>>>>>> conserved for this system. (of course there can also be an error in my
>>>>>>> hybrid monte carlo code, but the fact that the conserved energy is not
>>>>>>> conserved is disturbing me here)
>>>>>>>
>>>>>>>
>>>>>>> Servaas
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> What do you mean with effective energy?
>>>>>>> The Gromacs conserved energy term?
>>>>>>>
>>>>>>> For very small tau_t the current implementation does not work well.
>>>>>>> Bussi mailed me a proper implementation that I will put in when I have time.
>>>>>>>
>>>>>>> Berk
>>>>>>>
>>>>>>>
>>>>>>>> From: servaas.michielssens at student.kuleuven.be
>>>>>>>> To: gmx-users at gromacs.org
>>>>>>>> Date: Thu, 7 May 2009 09:02:52 +0200
>>>>>>>> Subject: [gmx-users] v-rescale - harmonic oscillator
>>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I did some experiments with a harmonic oscillator (diatomic molecule
>>>>>>>> without charge en LJ parameters) using the v-rescale thermostat. First I
>>>>>>>> ran a simulation in the NVE ensemble with a time-step of 0.0001ps, total
>>>>>>>> energy was constant here.
>>>>>>>>
>>>>>>>> Then I tried simulating the system with the v-rescale thermostat, same
>>>>>>>> time-step of 0.0001ps and tau_t=100,10,1,0.1,0.01,0.001. For none of
>>>>>>>> those simulations the effective energy was conserved.
>>>>>>>> (effective energy should be a conserved quantity for NVT simulations
>>>>>>>> with v-rescale thermostat, JOURNAL OF CHEMICAL PHYSICS Volume: 126
>>>>>>>> Issue: 1 Article Number: 014101 Published: JAN 7 2007 )
>>>>>>>>
>>>>>>>> So what is going wrong here? Would one expect this thermostat to fail
>>>>>>>> for such system (e.g. a simple Nose-Hoover is known to fail for the
>>>>>>>> harmonic oscillator)?
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks in advance,
>>>>>>>>
>>>>>>>> Servaas
>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
>>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 8 May 2009 11:36:05 +0200
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] Re: v-rescale - harmonic oscillator
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <COL113-W284BF26576BA5D3235474A8E640 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi,
>
> That is a fundamental problem of most global thermostats,
> just like Nose-Hoover. Nose-Hoover chains solve this.
> The only thermostats that guarantee proper ensembles for any system
> are local ones such as Langevin dynamics.
>
> Berk
>
>
>> From: servaas.michielssens at student.kuleuven.be
>> To: gmx-users at gromacs.org
>> Date: Fri, 8 May 2009 11:17:33 +0200
>> Subject: [gmx-users] Re: v-rescale - harmonic oscillator
>>
>> Hi,
>>
>> Thanks for your confirmation of this problem. One thing is not clear to
>> me from your answer. Has v-rescale fundamental problems with a Harmonic
>> oscillator or is it a problem with the GROMACS implementation?
>>
>>
>> Kind regards,
>>
>> Servaas
>>
>>
>>
>>> Message: 3
>>> Date: Fri, 8 May 2009 10:12:45 +0200
>>> From: Berk Hess <gmx3 at hotmail.com>
>>> Subject: RE: [gmx-users] Re: v-rescale - harmonic oscillator
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Message-ID: <COL113-W10F68330EA113929CBC3518E640 at phx.gbl>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>>
>>> Hi,
>>>
>>> I have come to the conclusion that the v-rescale thermostat is only correct
>>> in the limit of large numbers of degrees of freedom, which is equivalent to a small scaling limit.
>>> The conservation of the conserved energy quantity improves as the system gets bigger.
>>>
>>> But I noticed that in 4.0 the energy conservation is not good.
>>> It can be improved significantly by changing line 164 or src/mdlib/update.c from
>>> vv = lg*(vn + f[n][d]*w_dt);
>>> to
>>> vv = lg*vn + f[n][d]*w_dt;
>>>
>>> There are some other similar lines in case you are PR p-coupling or cosine acceleration.
>>>
>>> I will probably not fix this for 4.0.5, but only for 4.1, so we do not change
>>> the reproducibility in minor revisions.
>>>
>>> Berk
>>>
>>>
>>>
>>>> From: servaas.michielssens at student.kuleuven.be
>>>> To: gmx-users at gromacs.org
>>>> Date: Thu, 7 May 2009 15:27:37 +0200
>>>> Subject: [gmx-users] Re: v-rescale - harmonic oscillator
>>>>
>>>> Hi Berk,
>>>>
>>>> Thank you for your concern on this issue. It did not expect it to be a
>>>> problem from the paper of Bussi et al., but it is of course possible.
>>>> I am very curious to hear what they have to say about this. Are you
>>>> contacting him or will I do it?
>>>>
>>>> For the rotational degrees of freedom would removing them with
>>>> comm_mode=angular be a problem then because you are using restraints?
>>>> (you use orire than?)
>>>>
>>>> Thanks again,
>>>>
>>>> Servaas
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> With a diatomic molecule there is the issue that the rotation of the molecule has two degrees of freedom
>>>>> which are completely uncoupled from the rest of the system.
>>>>>
>>>>> Anyhow, I made a 1D harmonic oscillator using a position restraint and even there the energy
>>>>> does not seem to be conserved.
>>>>> I am not sure if a harmonic oscillator is a pathetic case, like with Nose-Hoover,
>>>>> or if this is an issue with the integrator implementation in Gromacs.
>>>>> I might need to ask Bussi about this.
>>>>>
>>>>> Berk
>>>>>
>>>>>
>>>>>> From: servaas.michielssens at student.kuleuven.be
>>>>>> To: gmx-users at gromacs.org
>>>>>> Date: Thu, 7 May 2009 14:03:30 +0200
>>>>>> Subject: [gmx-users] v-rescale - harmonic oscillator
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> It is just a diatomic molecule without other interactions (so only
>>>>>> bonded interaction, LJ=0 and charges=0 on the atoms). What other details
>>>>>> would you like to know? Should I send you the tpr file?
>>>>>>
>>>>>> Servaas
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> No, only for small values is should be off, maybe tau_t < 10 or 100 * delta_t.
>>>>>>>
>>>>>>> How did you set up your harmonic oscillator?
>>>>>>>
>>>>>>> Berk
>>>>>>>
>>>>>>>
>>>>>>>> From: servaas.michielssens at student.kuleuven.be
>>>>>>>> To: gmx-users at gromacs.org
>>>>>>>> Date: Thu, 7 May 2009 12:54:54 +0200
>>>>>>>> Subject: [gmx-users] Re: v-rescale - harmonic oscillator
>>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> Thank you for your reply.
>>>>>>>>
>>>>>>>> Yes by effective energy I mean the Gromacs conserved energy term.
>>>>>>>>
>>>>>>>> So you would say the cause of my problem here is that I need a small
>>>>>>>> tau_t to thermostat this system but for small tau_t values the algorithm
>>>>>>>> is not 100% ok yet? And what are very small tau_t values? I tested with
>>>>>>>> quite a big range here.
>>>>>>>>
>>>>>>>> The problem occurred to me when I was experimenting with a hybrid monte
>>>>>>>> carlo algorithm. I first tested it on a noble gas and compared to MD
>>>>>>>> simulation with nose-hoover and v-rescale. Those results were 100%
>>>>>>>> identical. Then I tried it on a dipeptide in vacuum, results were a
>>>>>>>> little off here (I would expect this for nose-hoover thermostat, but not
>>>>>>>> for v-rescale). So I decided to go the the extreme simple case of a
>>>>>>>> harmonic oscillator. Those results were seriously off, and then I
>>>>>>>> checked the conserved energy term, which seems impossible to keep it
>>>>>>>> conserved for this system. (of course there can also be an error in my
>>>>>>>> hybrid monte carlo code, but the fact that the conserved energy is not
>>>>>>>> conserved is disturbing me here)
>>>>>>>>
>>>>>>>>
>>>>>>>> Servaas
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> What do you mean with effective energy?
>>>>>>>> The Gromacs conserved energy term?
>>>>>>>>
>>>>>>>> For very small tau_t the current implementation does not work well.
>>>>>>>> Bussi mailed me a proper implementation that I will put in when I have time.
>>>>>>>>
>>>>>>>> Berk
>>>>>>>>
>>>>>>>>
>>>>>>>>> From: servaas.michielssens at student.kuleuven.be
>>>>>>>>> To: gmx-users at gromacs.org
>>>>>>>>> Date: Thu, 7 May 2009 09:02:52 +0200
>>>>>>>>> Subject: [gmx-users] v-rescale - harmonic oscillator
>>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I did some experiments with a harmonic oscillator (diatomic molecule
>>>>>>>>> without charge en LJ parameters) using the v-rescale thermostat. First I
>>>>>>>>> ran a simulation in the NVE ensemble with a time-step of 0.0001ps, total
>>>>>>>>> energy was constant here.
>>>>>>>>>
>>>>>>>>> Then I tried simulating the system with the v-rescale thermostat, same
>>>>>>>>> time-step of 0.0001ps and tau_t=100,10,1,0.1,0.01,0.001. For none of
>>>>>>>>> those simulations the effective energy was conserved.
>>>>>>>>> (effective energy should be a conserved quantity for NVT simulations
>>>>>>>>> with v-rescale thermostat, JOURNAL OF CHEMICAL PHYSICS Volume: 126
>>>>>>>>> Issue: 1 Article Number: 014101 Published: JAN 7 2007 )
>>>>>>>>>
>>>>>>>>> So what is going wrong here? Would one expect this thermostat to fail
>>>>>>>>> for such system (e.g. a simple Nose-Hoover is known to fail for the
>>>>>>>>> harmonic oscillator)?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks in advance,
>>>>>>>>>
>>>>>>>>> Servaas
>>>>>>>>>
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
>>>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> _________________________________________________________________
> What can you do with the new Windows Live? Find out
> http://www.microsoft.com/windows/windowslive/default.aspx
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090508/6e093508/attachment.html
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 61, Issue 29
> *****************************************
>
--
Jacek Czub, Ph.D.
Department of Theoretical and Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11, 37077 Göttingen, Germany
phone: +49(551)201-2323 fax: +49(551)201-2302
More information about the gromacs.org_gmx-users
mailing list