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)? 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 <[email protected]> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Quaerendo Invenietis-Seek and you shall discover.
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