[gmx-users] PMF and Gromacs 4

[Justin A. Lemkul]

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?
> 
>  

I already addressed this a few days ago:

http://lists.gromacs.org/pipermail/gmx-users/2009-October/046291.html

The statement in the manual about -pi, -pn, and -po is incorrect and needs to be 
updated.  The -pd option exists, but it is used for particle decomposition, and 
is not specifically related to the pull code.

So, to be clear, .ppa and .pdo files no longer exist in Gromacs 4, as the code 
and implementation has been completely changed since Gromacs 3.3.x.  See also:

http://manual.gromacs.org/current/online/mdp_opt.html#pull

-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

========================================