[gmx-users] LINCS vs SHAKE

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto: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
>     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

========================================