[gmx-users] LINCS vs SHAKE

Mark Abraham mark.abraham at anu.edu.au
Mon Nov 1 00:35:03 CET 2010 


----- Original Message -----
From: Sai Pooja <saipooja at gmail.com>
Date: Monday, November 1, 2010 10:24
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Some information:
> Except for this note, I do not get any other warning when I generate the  .tpr files. The cut-offs are in line with the forcefield  recommendations and 
>  The largest charge group contains 12 atoms.
>    Since atoms only see each other when the centers of geometry of the charge
>    groups they belong to are within the cut-off distance, too large charge
>    groups can lead to serious cut-off artifacts.
>    For efficiency and accuracy, charge group should consist of a few atoms.
>    For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc

Probably not critical, but IIRC the latest GROMACS imposes single-atom charge groups for CHARMM, in line with CHARMM developer advice.

> 
> @JJ
> 
> I am currently using Nose-hoover and it does happen close to a replica-exchange. Since I am attempting an algorithm which only scales the temperature of the protein and not the solvent across replicas, your pointer on the thermostat seems very pertinent.

Yep. That's a prime source for problems - IIRC post-exchange velocities are rescaled globally, not group-wise. Even if the latter were implemented, you'd still have to reconcile the fact that your simulations constantly have heat flowing from the solute heat bath to the solvent heat bath via your system. Is that sound?

Also, I'm not sure which temperature GROMACS is taking as the replica temperature, whether that is dependent on the order of the temperature-coupling groups in the .mdp file, and whether it shouldn't be regarding your situation as questionable/illegal and complaining at the grompp stage.

> Do you think a weaker coupling algo like Berendsen might help resolve this problem? 
> 
> I can also try using a smaller temperature range. I am currently using 300-900K (with solvent set at 300 for all 6 replicas). Perhaps if I use a smaller temperature range like 300-550, this could be prevented?

If that's the cause, then the answer is "probably", but you should address the underlying problem/question as above.

Mark

>    
> Pooja
> 
> On Sun, Oct 31, 2010 at 7:13 PM,  <thompsjj at purdue.edu> wrote:
>   Have you looked into changing the thermostat yet? Can you determine if the malformed residues are a result of a recent replica exchange? This continues to sound like an overheat that the thermostat cannot handle.  > 
 > 
 > 
 > 
 > 
 > 
 > 
>  Quoting Mark Abraham <mark.abraham at anu.edu.au>:
 > 
  > 
 > 
>  ----- 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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