[gmx-users] How to calculate the PMF?

[Justin A. Lemkul]

lammps lammps wrote:
> Dear all,
>  
> It is the first time that I use gromacs 4.04 to calculate PMF. I have 
> some question needed to be clarified.
>  
> 1. 
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> ; pull code for PMF
> pull                            = Unbrella        ;unbrella,constraint
> pull_geometry             = Distance        ;distance 
> ,direction,cylinder,position
> pull_dim                     = N N Y
> pull_group0                 = DPPC
> pull_group1                 = DEN
> pull_nstxout                = 100
> pull_nstfout                 = 100
> pull_init1                     = 3.8
> pull_k1                       = 1000 
>  
> Is there any relationship between the steps for pull_nstxout and 
> pull_nsfout. Must they be the same( e.g. 100, 100)? How to choose them?
>  

They do not have to be the same.  The values set depend on how many data points 
you want in the pullf.xvg and pullx.xvg files.

> 2. It seems that there are only two output file: pullx.xvg and 
> pullf.xvg. Is it right?  are there other files for the input of g_wham?
>  

The .tpr files used for the different sampling windows are passed to g_wham. 
See g_wham -h for the details.

-Justin

> 3. What other thing I must take care of for calculation of PMF
>  
> Thanks in advance.
> 
> -- 
> wende
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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