[gmx-users] free energy decomposition[David Van der Spoel]
msanku65 at yahoo.com
Fri Oct 15 05:59:08 CEST 2010
I was trying to understand your comments little bit carefully. If it is a NVT
ensemble simulation, then enthalpy becomes equal to potential energy ( as the
work due to volume-change is zero ).
But, I was wondering about your other comment: i.e. if it is constraint method,
the potential energy for each windows can be used directly from g_energy , BUT
if it is umbrella sampling, it will not be possible.
I guess,you may be saying this because, in umbrella sampling, an external
biasing potential is always being added to the total potential energy and so one
need to *unbias* it somehow to get the total potential energy ( which is not the
case for constraint method. )
But, my question is :
is there any way in gromacs that this biasing potential due to the umbrella
potential can be subtracted from the total potential energy ?
For example, use of g_energy on ener.edr file of one of the windows of an
umbrella sampling method shows following functionality: I was wondering if
subtracting functionality 11 (COM-Pull-En. ) from functionality 12 ( Potential
energy ) will provide unbiased potential energy .
1 Bond 2 Angle 3 U-B 4 Ryckaert-Bell.
5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR)
9 Coulomb-(SR) 10 Coul.-recip. 11 COM-Pull-En. 12 Potential
13 Kinetic-En. 14 Total-Energy 15 Conserved-En. 16 Temperature
17 Pressure-(bar) 18 Cons.-rmsd-() 19 Vir-XX 20 Vir-XY
21 Vir-XZ 22 Vir-YX 23 Vir-YY 24 Vir-YZ
25 Vir-ZX 26 Vir-ZY 27 Vir-ZZ 28 Pres-XX-(bar)
29 Pres-XY-(bar) 30 Pres-XZ-(bar) 31 Pres-YX-(bar) 32 Pres-YY-(bar)
33 Pres-YZ-(bar) 34 Pres-ZX-(bar) 35 Pres-ZY-(bar) 36 Pres-ZZ-(bar)
37 #Surf*SurfTen 38 Mu-X 39 Mu-Y 40 Mu-Z
41 T-System 42 Xi-System
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wed, October 13, 2010 1:42:41 PM
Subject: Re: [gmx-users] free energy decomposition
On 10/13/10 8:30 PM, Chris Neale wrote:
> This is not possible using g_energy or any other gromacs tool that I am aware
> You must calculate the temperature derivative of the free energy.
> See, for example, equation 16 in Pettitt BM, Rossky PJ. J Chem Phys.
Recent versions of gromacs will actually plot the enthalpy in the energy
file, and since your are only interested in the enthalpy difference that
would work *if it wasn't for the umbrella sampling*. I think if you had
used constraints rather than umbrellas this might do the trick.
Temperature dependence is of course a dependable way as well.
> -- original message --
> I am studying Potential of mean force(PMF) of association of two peptides. I
> want to decompose the PMF into energy(enthalpy) and entropic terms. But, I
> some queries on how to extract those contributions .
> I found, in literature, generally, people try to get the energy(enthalpy)
> first and then subtract it from PMF to get the entropic contribution. My
> question is related to how to get the energy term first:
> 1. Will it be appropriate to just use g_energy tool on ener.edr file for each
> windows obtained from umbrella sampling and select the 'potential energy'
> functionality term to get the*average potential energy* for each windows ?
> I used energy groups = system in the .mdp file for each windows of my
> sampling simulations.
> 2. If it is so, now I wonder whether g_energy will give that potental energy
> *in presence of umbrella bias* . If it is true, do one need to first unbias
> energy some how ( like using a boltzman factor) ? However, I do not how to do
> if you provide any ideas, that will be great .
> Here is the details on what I have done to get the PMF .
> I am studying Potential of mean force(PMF) of association of two peptides.
> this purpose , I have carried out GROMACS 4.0.7 umbrella sampling simulation
> dividing the reaction coordinate( i.e distance between center of mass of two
> peptides) into around 25 windows of 0.1 nm separation. Now, I have used WHAM
> and got the PMF by unbiasing the umbrella potential.
David van der Spoel, PhD, Professor of Biology
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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