Rebeca García Fandiño wrote:
Thank you very much for the suggestion.
Actually, I am trying to reproduce the results from another publication
(JACS 2005, 127, 7166) http://pubs.acs.org/doi/full/10.1021/ja050044d
where they used Gromacs/amber to simulate a CNT. They apply:
"Carbon−carbon bond lengths of 0.14 nm and bond angles of 120° were
maintained by harmonic potentials with spring constants of 393 960 kJ
mol^- ^1 nm^- ^2 and 527 kJ mol^- ^1 deg^- ^2 before relaxation. In
addition, a weak dihedral angle potential was applied to bonded carbon
atoms.^"
So, as I understand, they apply RESTRAINTS to the bonds, angles and
dihedrals.
Well, they used potential forms similar to those used in restraints. One
can use a harmonic "bond" potential (function type 6 IIRC) in GROMACS
without using a distance restraint. See table 5.4.
I have tried to construct the [distance_restraints] for my system (I
show you here a little part):
[ distance_restraints ]
; atom1 atom2 type index type2 low up1 up2 fac
1 310 1 1 1 0.142 0.146 0.150 1.0
2 290 1 2 1 0.142 0.146 0.150 1.0
3 291 1 3 1 0.142 0.146 0.150 1.0
(...)
but I don' t understand very well which value should I write for "low
up1 up2". The manual says that "the columns low, up1 and up2 hold the
values of r0 , r1 and r2 from eqn. 4.76", but looking at this equation I
still don' t understand which should be the better values for my case. I
have looked into the mail archive, and some other people asked for that,
but I did not find any proper solution.
How could I choose the best values for "low up1 up2" to restrain my
bond values to 1.42 Amstrong?
The other question is about angle restraints, I have found indications
in the wiki of how to treat the dihedral restraints
(http://wiki.gromacs.org/index.php/Dihedral_Restraints), however I did
not find any similar for the angle restraints. I have seen in the mail
archive that 2 pairs of atoms should be used, but I did not find
anything to trust in. Could you please give me some indications of how
to treat angle restraints?
Section 4.3.2 and Table 5.5 seem to cover it, I think.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
