I think Mark's comment still stands in this case: the argument for keeping the bath and the protein at different, nonequilibrating temperatures is still unsound. It might not explode right away, because by lowering the timestep and decreasing temperature, you're affording the thermostat a better chance to try to scale back velocities. Explode or not, at 500K the solute is still pumping large amounts of energy into the 300K solvent, which you're asking the thermostat to absorb. The physics at the solute-solvent boundary are questionable at best - real-life atoms don't get to have a special thermostat to rescale velocities when they touch something hot.

~j

Quoting Sai Pooja <saipo...@gmail.com>:

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, <thomp...@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.abra...@anu.edu.au>:



----- Original Message -----
From: Sai Pooja <saipo...@gmail.com>
Date: Monday, November 1, 2010 10:24
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users <gmx-users@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,  <thomp...@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.abra...@anu.edu.au>:

 >
 >
 >

 ----- Original Message -----
 From: Sai Pooja <saipo...@gmail.com>
 Date: Monday, November 1, 2010 8:12
 Subject: Re: [gmx-users] LINCS vs SHAKE
 To: Discussion list for GROMACS users <gmx-users@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 <jalem...@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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