Rebeca García Fandiño wrote:
Hello,
I would like to simulate a CNT and I want to apply a harmonic potential:
-on the C-C bonds
-on the bond angles
-on the dihedral angles
with a different spring constant for each case.
I have read Section 4.3 from Gromacs manual, but I actually have some
doubts about how to include this in the topology.
-for the distance restraints I have tried to use genrestr:
genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 400000
The file I obtain is something like:
; distance restraints for UNK of cnt_wat_gmx.gro created by
rdparm2gmx.pl Wed May 20 10:20:59 BST 2009
[ distance_restraints ]
; i j ? label funct lo up1 up2 weight
1 2 1 0 1 0.403354 0.603354 1.60335 1
1 3 1 1 1 0.587676 0.787676 1.78768 1
1 4 1 2 1 0.769212 0.969212 1.96921 1
1 5 1 3 1 0.86081 1.06081 2.06081 1
(...)
This is different from the [distance_restraint] example shown in pag 69
of the manual, now I don' t have the fac column. I would like to apply a
The format of the distance_restraints section appears correct. If you read the
description of the "fac" column, it is a weighting factor for that particular
restraint. So therefore, "weight" is probably equivalent.
spring constant of 400000 to C-C bonds, but where is the constant here?
How could I apply a determined spring constant? In the .mdp file?
Besides, all the distances are restrained... Is there any way to
restrain only the C-C bonds? I mean I don' t want to restrain the
distance between a carbon and a carbon far away from it, only
restraining the neighbouring carbons to a distance of 1.4 A.
You cannot use genrestr for this purpose. Using genrestr -disre generates a
matrix of all atoms you specify. Also, -fc is expected to be used with position
restraints; note the format given in genrestr -h.
Are you really interested in applying restraints to all bonds, angles,
dihedrals, and distances? Realize that constraints (Section 5.5) and restraints
are separate ideas in Gromacs.
If you want to define your own force constants for bonds, angles, etc. simply do
so in the topology yourself (Table 5.4).
-Justin
Another question is: Is there any tool to construct the equivalent
angle_restraints and dihedral_restraints in an authomatic way, or should
I do it by hand?
Thank you very much in advance for your help.
Best wishes,
Dr. Rebeca Garcia
Parc Cientific de Barcelona
Spain
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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