[gmx-users] PMF calculation with constraint distance

Justin Lemkul jalemkul at vt.edu
Thu May 21 23:04:33 CEST 2015

On 5/21/15 5:00 PM, leila salimi wrote:
> Hi all,
> I started to calculate PMF between two ions in solution and I
> used constraint for pull option, instead of umbrella as I saw in Umbrella
> sampling Tutorial of Justin.
> This is the part of my mdp file!
> ; Pull code
> pull            = constraint    ; Justin's value was "umbrella"
> pull_geometry   = distance      ; simple distance increase
> pull_dim        = Y Y Y
> pull_start      = no            ; Justin's value was "yes"
> pull_ngroups    = 1
> pull_group0     = CA_surf
> pull_group1     = carboxylate_carbon
> pull_init1      = 0.288         ; initial distance between pulling groups
> pull_rate1      = 0.001 ; 0.001 nm per ps
> pull_k1         = 1000          ; kJ mol^-1 nm^-2
> I got the output  and I tried to pull out with increasing  the distance
> between two atoms and I have pullf.xvg file!
> I know that I can have the time evolution of constrained distance with
> g_dist from xtc file! I am wondering how to have the distance with
> corresponding constrained force?
> If I have the file contain forces and distances, I can integrate the force
> then I will have PMF.

This probably won't give you a very reliable PMF.  You're effectively trying to 
use the Jarzynski method (albeit with a constraint rather than a harmonic 
potential) with one run (normally you have to do this many, many times), which 
won't give a correct result.

> Could you help me that how I can manage this?

If you have the constraint force in pullf.xvg and the distance in another .xvg 
file, it's just a matter of using grep/awk to combine the two.  Whether or not 
this means anything is another matter.  Getting a PMF between ions is trivially 
simple with a harmonic potential.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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