<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Hi David,</div><div> </div><div> 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 ).</div><div>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.</div><div> 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.
) </div><div> But, my question is :</div><div>is there any way in gromacs that this biasing potential due to the umbrella potential can be subtracted from the total potential energy ? </div><div><br></div><div>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 .</div><div><br></div><div><div>1 Bond 2 Angle 3 U-B 4 Ryckaert-Bell.</div><div> 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR)
</div><div> 9 Coulomb-(SR) 10 Coul.-recip. 11 COM-Pull-En. 12 Potential </div><div> 13 Kinetic-En. 14 Total-Energy 15 Conserved-En. 16 Temperature </div><div> 17 Pressure-(bar) 18 Cons.-rmsd-() 19 Vir-XX 20 Vir-XY </div><div> 21 Vir-XZ 22 Vir-YX 23 Vir-YY 24 Vir-YZ </div><div> 25 Vir-ZX 26 Vir-ZY 27 Vir-ZZ 28 Pres-XX-(bar) </div><div> 29 Pres-XY-(bar) 30
Pres-XZ-(bar) 31 Pres-YX-(bar) 32 Pres-YY-(bar) </div><div> 33 Pres-YZ-(bar) 34 Pres-ZX-(bar) 35 Pres-ZY-(bar) 36 Pres-ZZ-(bar) </div><div> 37 #Surf*SurfTen 38 Mu-X 39 Mu-Y 40 Mu-Z </div><div> 41 T-System 42 Xi-System</div></div><div><br></div><div><br></div><div>Sanku</div><div> </div><div><br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> David van der Spoel <spoel@xray.bmc.uu.se><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for
GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wed, October 13, 2010 1:42:41 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] free energy decomposition<br></font><br>
On 10/13/10 8:30 PM, Chris Neale wrote:<br>> Sanku,<br>><br>> This is not possible using g_energy or any other gromacs tool that I am aware of.<br>> You must calculate the temperature derivative of the free energy.<br>> See, for example, equation 16 in Pettitt BM, Rossky PJ. J Chem Phys. 1986;84:5836<br>><br>Recent versions of gromacs will actually plot the enthalpy in the energy <br>file, and since your are only interested in the enthalpy difference that <br>would work *if it wasn't for the umbrella sampling*. I think if you had <br>used constraints rather than umbrellas this might do the trick.<br><br>Temperature dependence is of course a dependable way as well.<br><br>> -- original message --<br>><br>> Hi,<br>><br>> I am studying Potential of mean force(PMF) of association of two peptides. I<br>> want to decompose the PMF into energy(enthalpy) and entropic terms. But, I have<br>> some queries on how
to extract those contributions .<br>><br>><br>> I found, in literature, generally, people try to get the energy(enthalpy)<br>> first and then subtract it from PMF to get the entropic contribution. My<br>> question is related to how to get the energy term first:<br>><br>> 1. Will it be appropriate to just use g_energy tool on ener.edr file for each<br>> windows obtained from umbrella sampling and select the 'potential energy'<br>> functionality term to get the*average potential energy* for each windows ?<br>> I used energy groups = system in the .mdp file for each windows of my umbrella<br>> sampling simulations.<br>><br>> 2. If it is so, now I wonder whether g_energy will give that potental energy<br>> *in presence of umbrella bias* . If it is true, do one need to first unbias the<br>> energy some how ( like using a boltzman factor) ? However, I do not
how to do<br>> that.<br>><br>> if you provide any ideas, that will be great .<br>><br>> Here is the details on what I have done to get the PMF .<br>><br>> I am studying Potential of mean force(PMF) of association of two peptides. For<br>> this purpose , I have carried out GROMACS 4.0.7 umbrella sampling simulation by<br>> dividing the reaction coordinate( i.e distance between center of mass of two<br>> peptides) into around 25 windows of 0.1 nm separation. Now, I have used WHAM<br>> and got the PMF by unbiasing the umbrella potential.<br>><br>> Sanku<br>><br>><br><br><br>-- <br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Professor of Biology<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471
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