[gmx-users] LINCS vs SHAKE

[thompsjj at purdue.edu]

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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