[gmx-users] LINCS vs SHAKE

[Sai Pooja]

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

@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.

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?

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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-- 
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