[gmx-users] bond, angle and dihedral restraints in Gromacs

[Justin A. Lemkul]

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
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------
> Haz búsquedas con Live Search, ¡todas tus búsquedas tienen premio! 
> <http://www.buscalasuerte.com/>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================