[gmx-users] options in mdp for PMF

[Justin A. Lemkul]

Rebeca García Fandiño wrote:
> 
>  Hi,
> I would like to calculate the PMF of an ion along a channel using 
> Gromacs 4, and I have a doubt about the options I should use in the .mdp 
> file:
>  
> -which option should I choose for pull_geometry: distance? direction? or 
> position?

If you're intending on using g_wham to calculate PMF, you must use distance.

> -which is the equivalent option to the old "Pos1" (in Gromacs 3) for the 
> Gromacs 4 version?

Set "pull_start = yes" and "pull_init = 0" to restrain the pull group at the 
original COM distance from the reference.

-Justin

>  
> Thank you very much for your help.
> Best wishes,
>  
> Rebeca Garcia Fandiño
> Oxford Universtity
> UK
> 
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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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