Ania, ja nie wzialem laptopa dla Ciebie :-( wezmiesz go ? :-* gmx-users-requ...@gromacs.org wrote: > Send gmx-users mailing list submissions to > gmx-users@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-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@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.va...@gmail.com> > Subject: [gmx-users] x2top and OPLS-AA vs. fudged 1-4 interactions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <91220afc0905080207vc411cf5of28da3eddb73e...@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.michielss...@student.kuleuven.be> > Subject: [gmx-users] Re: v-rescale - harmonic oscillator > To: gmx-users@gromacs.org > Message-ID: <1241774253.6575.2.ca...@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 <g...@hotmail.com> >> Subject: RE: [gmx-users] Re: v-rescale - harmonic oscillator >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: <col113-w10f68330ea113929cbc3518e...@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.michielss...@student.kuleuven.be >>> To: gmx-users@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.michielss...@student.kuleuven.be >>>>> To: gmx-users@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.michielss...@student.kuleuven.be >>>>>>> To: gmx-users@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@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 >>>>>>> > > > > > ------------------------------ > > Message: 3 > Date: Fri, 8 May 2009 11:36:05 +0200 > From: Berk Hess <g...@hotmail.com> > Subject: RE: [gmx-users] Re: v-rescale - harmonic oscillator > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <col113-w284bf26576ba5d3235474a8e...@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.michielss...@student.kuleuven.be >> To: gmx-users@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 <g...@hotmail.com> >>> Subject: RE: [gmx-users] Re: v-rescale - harmonic oscillator >>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>> Message-ID: <col113-w10f68330ea113929cbc3518e...@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.michielss...@student.kuleuven.be >>>> To: gmx-users@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.michielss...@student.kuleuven.be >>>>>> To: gmx-users@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.michielss...@student.kuleuven.be >>>>>>>> To: gmx-users@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@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 list gmx-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 >> > > _________________________________________________________________ > 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@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 _______________________________________________ gmx-users mailing list gmx-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