[gmx-users] PMF and Gromacs 4

Rebeca García Fandiño regafan at hotmail.com
Sun Nov 1 15:27:19 CET 2009


I am trying to calculate the PMF of an ion with Gromacs 4. I have read in the Gromacs list that the pull code had been completely rewritten in the new version of Gromacs, but I cannot find much information about the new way to use this.
Reading the manual (pag 280) I can see: “The options -pi, -po, -pd, -pn are used for potential of mean force calculations and umbrella sampling. See manual.”
So, I prepared a tpr and a .ppa file and tried the calculation and used (for example for one window):
source /gpfs/apps/GROMACS/gromacs-4.0.2/bin/GMXRC
srun -n 8 mdrun_s -v -stepout 1000 -s NA-0.0250.tpr -pi NA-0.0250.ppa -po pullout.ppa -pn NA-0.0250.ndx -pd -deffnm NA-0.0250
gzip NA-0.0250.pdo
Being NA-0.0250.ppa:
verbose   = yes
runtype   = umbrella     
pulldim   = N N Y         
reftype   = com        
reference_group = UNK    

group_1   = Na_-0.025

K1        = 970.86;           ; kJ / (mol nm^2)
Pos1      = 0.000 0.000 -0.025  ; centre of the umbrella potential
I don´t get any errors during the calculation, however, I did not get any out files such as *.pdo.
I only get the *cpt, *trr, *log and *edr files after the calculation, but no signal of *pdo.
Does anyboy had used Gromacs 4 for calculating PMF? Am I doing something wrong?
Thank you very much for your help.
Best wishes,
Rebeca Garcia.
Santiago de Compostela University

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