[gmx-users] LINCS vs SHAKE

Sai Pooja saipooja at gmail.com
Sun Oct 31 22:12:09 CET 2010

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.


On Sat, Oct 30, 2010 at 3:40 PM, Justin A. Lemkul <jalemkul at 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
> 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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Quaerendo Invenietis-Seek and you shall discover.
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