Rebeca García Fandiño wrote:
Hi,
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?
Yes, the pull parameters are all specified in the .mdp file now, so you can't
supply a .ppa file. Unfortunately, mdrun does not check for unrecognized flags
(like -pi, -pn, etc).
Are you reading the right version of the manual? I can find no mention of these
old flags in the manual for version 4.
See version 4 manual, section 7.3.21 for COM pulling options.
-Justin
Thank you very much for your help.
Best wishes,
Rebeca Garcia.
Santiago de Compostela University
Spain.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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