[gmx-users] Re: freeze value

Justin Lemkul jalemkul at vt.edu
Wed Sep 12 15:42:34 CEST 2012

On 9/12/12 4:52 AM, samira ansari wrote:
> Dear justin,
> I have a problem with freezing group. I got no answer from gmx_users.

I don't recall seeing the original post.  In any case, please keep any 
Gromacs-related correspondence on the mailing list; I am not a private help 
service.  I am CC'ing this message to the list and ask that anything further be 
posted there.

> I made three group Fflex rigid1 rigid2 in my index
> I changed the fx, fy, fz of atoms belong to rigid1 and rigid2 in .itp file after
> pdb2gmx.

Assuming these are x,y,z force constants in posre.itp, they are irrelevant. 
Position restraints and freezing are different concepts and different algorithms 

> also I made this part in em.mdp file:
> ; freezing group
> energygrp_excl      = rigid1 rigid1 rigid1 SOL rigid2 rigid2 rigid2 SOL ! To remove
> ;computation of nonbonding interactions between the frozen groups with each
> other and surroundings (i.e. the solvent, SOL)

An exclamation point on this line may cause problems.

> freezegrps          =  rigid1 rigid2
> freezdim            =  Y Y Y Y Y Y
>   but during grompp it shows fatal error:
> Invalid Freezing input: 2 groups and 0 freeze values
> what should I do to solve this problem?

You may have some issue with line endings.  Make sure you are always using a 
plain text editor and make use of dos2unix if necessary.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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