Sai Pooja wrote:
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.


There have been a number of replies to your question that have provided good ideas for you to investigate. Something about your system is becoming unstable, but without seeing your .mdp file there's nothing but guesswork to be done.

-Justin

Pooja

On Sat, Oct 30, 2010 at 3:40 PM, Justin A. Lemkul <jalem...@vt.edu <mailto: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 <http://vt.edu> | (540) 231-9080
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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--
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

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