[gmx-users] PMF in 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?
> 
>  

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

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