[gmx-users] LINCS vs SHAKE

[Mark Abraham]

----- Original Message -----
From: Sai Pooja <saipooja at gmail.com>
Date: Monday, November 1, 2010 8:12
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users <gmx-users at 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 <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 | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 > 
>  ========================================
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