[gmx-users] free energy decomposition[David Van der Spoel]

Sanku M msanku65 at yahoo.com
Fri Oct 15 05:59:08 CEST 2010

Hi David,
  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:
> Sanku,
> 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 --
> Hi,
> 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
> that.
> 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.
> Sanku

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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