----- 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
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