[gmx-users] LINCS vs SHAKE
Sai Pooja
saipooja at gmail.com
Mon Nov 1 03:52:01 CET 2010
Thanks JJ and Mark. I shall revise my algorithm/technique. This was just a
lazy way of implementing a more robust technique and I shall use the more
rigorous form.
However, if one wants to use the current technique with a smaller
temperature range, the dynamics of the system with say Protein at 500K and
water at 300K would be unphysical or can that be corrected by using a
smaller timestep and thermostat type/parameters?
Pooja
On Sun, Oct 31, 2010 at 10:15 PM, <thompsjj at purdue.edu> wrote:
> I concur with Mark - you're pumping heat into the solvent which is
> physically unsound, particularly at the solute-solvent boundary in your
> situation. This would be analogous to making a block of metal at 900K
> instantly "appear" in water at 300K: what would happen?
> Technically the Nose-Hoover thermostat is going to be better than Berendsen
> at reducing the noncanonical bias in the replica exchange, but of course
> using a smaller range of temperatures is going to reduce the pressure on the
> thermostat to keep up with velocity scaling. This is a different problem
> entirely, though. To be honest, I see the difference in your management of
> protein and solvent temperatures as the biggest problem here.
>
>
>
> Quoting Mark Abraham <mark.abraham at anu.edu.au>:
>
>
>>
>> ----- 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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