[gmx-users] PMF in Gromacs 4

Rebeca García Fandiño regafan at hotmail.com
Thu Oct 29 20:38:25 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
Convierte las fotos que más te gustan en tu nuevo fondo de escritorio para el ordenador. Es fácil y además gratis
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091029/ed68361d/attachment.html>

More information about the gromacs.org_gmx-users mailing list