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
entirely.
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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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