[gmx-users] umbrella sampling

Justin Lemkul jalemkul at vt.edu
Sat Sep 2 23:19:56 CEST 2017

On 9/2/17 10:28 AM, spss4 at iacs.res.in wrote:
>   Hi all
> I am trying to do umbrella sampling of protein unfolding with radius of
> gyration as reaction coordinate using gromacs-2016.3 patched with
> plumed-2.3.2. I want to calculate free energy for the system. I am using
> the following command
> gmx wham P=1.4 1.5 100 0.001 300 0 metadata.dat  free.dat

None of this is valid syntax.

> It shows an error
>   Fatal error:
>   Give either pullx (-ix) OR pullf (-if) data. Not both.
> But I am using radius of gyration as variable.Why I need to give pullx ?
> Please anyone help.

gmx wham assumes you're using the GROMACS pull code, therefore relying entirely 
on GROMACS input and output files.  If you're doing something else, you're going 
to need to use another program (e.g. Alan Grossfield's WHAM program or whatever 
else the PLUMED community suggests).



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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