[gmx-users] REST variant of REMD

David van der Spoel spoel at xray.bmc.uu.se
Mon Jul 24 21:53:06 CEST 2006

Anthony Armstrong wrote:
> Hello all,
> I'd like to run REMD on a peptide system, but it turns out out my
> system is a little to large, and I've determined that to get a swap
> probablity of .2, a separation of temperature of only a couple degrees
> between replicas would be required.  I ran across the paper of Liu et al.
> (PNAS 2005 102:13749-13754) on Replica Exchange with Solute Tempering
> which addresses this problem and which appears to attempt temperature
> swaps based on a "modified" total potential in which solute/solute and
> solute/protein interactions are first scaled.

Are you sure you want to do this? All but one of your replicas become 
non-physical and you can not do fun stuff like extracting kinetics info 
from the trajectory anymore (see David van der Spoel and M. Marvin 
Seibert: Protein Folding Kinetics and Thermodynamics from Atomistic 
Simulations, Phys. Rev. Lett. 96 pp. 238102, 2006).

> My question is:
> How might I go about calculating a user defined energy (in this case
> E(X) = Ep(X) + A(T) * Ew(X) + B(T) * Epw -->  where X is the set of
> system coordinates, subscripts p, w, and pw denote protein/protein,
> water/water, and protein/water interactions, respectively, and A(T) and
> B(T) are scale factors involving the target temperature for the given
> replica) and then pass this energy rather than the unscaled potential
> to gromacs for determining whether or not to swap temperatures.
> Any help would be much appreciated.

The problem is in PME, for which you can not directly extract 
interaction energies. There is a solution for this, but it is not 
Otherwise everything is present, except for some additional parameters 
to determine your A and B functions.

> Thanks,
> Tony
> Anthony A. Armstrong
> Department of Biophysics and Biophysical Chemistry
> Johns Hopkins University School of Medicine
> 725 North Wolfe Street
> Baltimore, MD 21205
> 410-955-8715
> 410-955-0637 FAX
> armstron at groucho.med.jhmi.edu
> On Wed, 19 Jul 2006, Anthony Armstrong wrote:
>>I'm hoping to get some tips on removing protein rotation inside a
>>triclinic water box.  Apologies if this has been covered recently, but
>>the most recent discussion I've been able to track down is a thread from
>>2003 which stated a patch was available to prevent such rotations and an
>>algorithm would be formally implemented into GROMACS "in the near future"
>>(Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl Tue May 20 13:52:00 CEST
>>2003).  Has the implementation occurred?  If I use comm-grps = Protein and
>>comm-mode = angular?  Of course I'm in the process of trying it, but
>>thought some kind person from the Gromacs community might be able to save
>>me some time if it is going to fail.  Thanks in advance.
>>Anthony A. Armstrong
>>Department of Biophysics and Biophysical Chemistry
>>Johns Hopkins University School of Medicine
>>725 North Wolfe Street
>>Baltimore, MD 21205
>>410-955-0637 FAX
>>armstron at groucho.med.jhmi.edu
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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