Thanks JJ and Mark. I shall revise my algorithm/technique. This was just a lazy way of implementing a more robust technique and I shall use the more rigorous form. However, if one wants to use the current technique with a smaller temperature range, the dynamics of the system with say Protein at 500K and water at 300K would be unphysical or can that be corrected by using a smaller timestep and thermostat type/parameters?
Pooja On Sun, Oct 31, 2010 at 10:15 PM, <thomp...@purdue.edu> wrote: > I concur with Mark - you're pumping heat into the solvent which is > physically unsound, particularly at the solute-solvent boundary in your > situation. This would be analogous to making a block of metal at 900K > instantly "appear" in water at 300K: what would happen? > Technically the Nose-Hoover thermostat is going to be better than Berendsen > at reducing the noncanonical bias in the replica exchange, but of course > using a smaller range of temperatures is going to reduce the pressure on the > thermostat to keep up with velocity scaling. This is a different problem > entirely, though. To be honest, I see the difference in your management of > protein and solvent temperatures as the biggest problem here. > > > > Quoting Mark Abraham <mark.abra...@anu.edu.au>: > > >> >> ----- Original Message ----- >> From: Sai Pooja <saipo...@gmail.com> >> Date: Monday, November 1, 2010 10:24 >> Subject: Re: [gmx-users] LINCS vs SHAKE >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> >> Some information: >>> Except for this note, I do not get any other warning when I generate the >>> .tpr files. The cut-offs are in line with the forcefield recommendations >>> and >>> The largest charge group contains 12 atoms. >>> Since atoms only see each other when the centers of geometry of the >>> charge >>> groups they belong to are within the cut-off distance, too large charge >>> groups can lead to serious cut-off artifacts. >>> For efficiency and accuracy, charge group should consist of a few >>> atoms. >>> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc >>> >> >> Probably not critical, but IIRC the latest GROMACS imposes single-atom >> charge groups for CHARMM, in line with CHARMM developer advice. >> >> >>> @JJ >>> >>> I am currently using Nose-hoover and it does happen close to a >>> replica-exchange. Since I am attempting an algorithm which only scales the >>> temperature of the protein and not the solvent across replicas, your pointer >>> on the thermostat seems very pertinent. >>> >> >> Yep. That's a prime source for problems - IIRC post-exchange velocities >> are rescaled globally, not group-wise. Even if the latter were implemented, >> you'd still have to reconcile the fact that your simulations constantly have >> heat flowing from the solute heat bath to the solvent heat bath via your >> system. Is that sound? >> >> Also, I'm not sure which temperature GROMACS is taking as the replica >> temperature, whether that is dependent on the order of the >> temperature-coupling groups in the .mdp file, and whether it shouldn't be >> regarding your situation as questionable/illegal and complaining at the >> grompp stage. >> >> Do you think a weaker coupling algo like Berendsen might help resolve >>> this problem? >>> >>> I can also try using a smaller temperature range. I am currently using >>> 300-900K (with solvent set at 300 for all 6 replicas). Perhaps if I use a >>> smaller temperature range like 300-550, this could be prevented? >>> >> >> If that's the cause, then the answer is "probably", but you should address >> the underlying problem/question as above. >> >> Mark >> >> >>> Pooja >>> >>> On Sun, Oct 31, 2010 at 7:13 PM, <thomp...@purdue.edu> wrote: >>> Have you looked into changing the thermostat yet? Can you determine if >>> the malformed residues are a result of a recent replica exchange? This >>> continues to sound like an overheat that the thermostat cannot handle. > >>> >> > >> > >> > >> > >> > >> > >> >>> Quoting Mark Abraham <mark.abra...@anu.edu.au>: >>> >> > >> > >> > >> >>> ----- Original Message ----- >>> From: Sai Pooja <saipo...@gmail.com> >>> Date: Monday, November 1, 2010 8:12 >>> Subject: Re: [gmx-users] LINCS vs SHAKE >>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>> >> > >> > Yes, I understand that. But then this is a protein in water simulation >> with CHarmm forcefield and I cannot find a reason as to why does this >> happen(esp after variable number of steps)? >> > >> >>> MD integrates equations of motion. If the starting configuration, or >>> integration procedure is not well-formed, then atoms will experience large >>> forces and motions, which lead to more, which eventually lead to a smoking >>> pile of debris. See >>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up for >>> discussion and suggestions >>> >> > >> >>> Mark >>> >> > >> > I have checked the .pdb files generated for the steps where Lincs >> fails and it seems that H atoms for atleast 1 sidechain are in incorrect >> positions(usually clashing). There doesn't seem to be a good way of >> analyzing this error. If you have any suggestions I would be eager to try >> them. >> > > >> > Pooja >> > >> >>> On Sat, Oct 30, 2010 at 3:40 PM, Justin A. Lemkul <jalem...@vt.edu> >>> wrote: >>> >> > > >> >>> > >>> >> > Sai Pooja wrote: >> > > >> > For Replica exchange, is there any advantage of in using SHAKE over >> LINCS(other than the stepsize)? >> >>> I am running an REM simulation and the simulation stops after running >>> for variable number of steps (100000, 10000000 etc.) because some bond moves >>> more than 30 degrees and LINCS gives a warning. >>> >> > > >> >>> > >>> >> > It has been said (check the archive) that LINCS is more stable. Just >> because you're getting LINCS warnings does not mean the constraint algorithm >> is to blame, it's just the first algorithm that fails when your model >> physics implodes. >> > > >> > -Justin >> > > >> >>> > >>> >> > Pooja >> > > >> > -- >> >>> Quaerendo Invenietis-Seek and you shall discover. >>> >> > > >> >>> > >>> >> > -- >> >>> ======================================== >>> >> > > >> > Justin A. Lemkul >> >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> >> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >>> > >>> >> > ======================================== >> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> >> > > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >> > > >> > > >> >>> -- >>> Quaerendo Invenietis-Seek and you shall discover. >>> >> > > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> >>> Please search the archive at >>> >> > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >> > >> > >> > >> > >> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use thewww >>> interface or send it to gmx-users-requ...@gromacs.org. > >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> > >> >>> > >>> -- >>> Quaerendo Invenietis-Seek and you shall discover. >>> >> > -- >> >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >> >> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Quaerendo Invenietis-Seek and you shall discover.
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