[gmx-users] Re: freeze value
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
> 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
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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