I am not sure what you are asking since I believe that I have already
given you this answer on the gromacs mailing list.
http://www.gromacs.org/pipermail/gmx-users/2006-December/025087.html
I certainly do not mind personal emails and I am happy to help, but
there are three very good reasons to keep everything on the gromacs
mailing list:
1. Answers may be read by people who disagree with portions of the
answer -- such as Mark's suggestion that my system's stability using a
dihedral restraint around 180deg was fortuitous and that you should
redefine your dihedral to avoid that.
http://www.gromacs.org/pipermail/gmx-users/2006-December/025089.html
2. I may not know the answer to your question but somebody else might.
3. The questions and answers are maintained for somebody else to
search through years later.
In fact, I don't know how to do exactly what you are suggesting. Do
you mean that at every integration step the dihedral feels a pull
toward it's 180deg opposite position? Or perhaps you want to do this
(using phiAtTimeZero instead of phi on the right side of the equation):
{ X [ A (1+cos (nT-phi)) ] } - { (1-X) [ A (1+cos (nT-( phiAtTimeZero
+ 180 ))) ] }
in place of the equation that you have written (below). In any event,
if what you are asking is how to slowly change the umbrella then you
could look into the afm pulling code and see if that is possible for
dihedrals. Otherwise, you could do what I have suggested previously
except that you should periodically stop and change the phi value of
your dihedral restraint in the .top file and then grompp to get the
updated tpr and then mdrun again. If you are asking how to use a cos
function and thus be able to use 180deg... then you have me stumped. I
also tried to do this but I think that it is not currently possible.
If you do use my previous suggestion then please note that there is no
guarantees that anything you do around a dihedral of about 180 using
the dihedral restraint will work (since it is not a cos function).
Therefore you should redefine the value. For example, I am working
similarly with a chi1 dihedral. For this I have the options of
N-CA-CB-CG or C'-CA-CB-CG. If I want N-CA-CB-CG to be at 180deg then
one could instead require that C'-CA-CB-CG be at 60 deg (check this
actual value for yourself though to ensure that I haven't slipped a
sign or rotated the wrong direction... this is all from my memory of
what I set up a while ago).
Please don't hesitate to send another email to the list if you have
some more questions on this topic.
Quoting Prasad Gajula <[EMAIL PROTECTED]>:
Dear Chris,
Thanks a lot for your answer. I dont know if iam disturbing you. Iam
very sorry for that.
Hope you can help me to solve my prolem.
i need to rotate a bond simultaneously from its present orientation
to opposite orientation.
my idea is like this...
the dihedral angle formula is
[ A (1+cos (nT-phi)) ] right.
now, i want to do like this...
{ X [ A (1+cos (nT-phi)) ] } - { (1-X) [ A (1+cos (nT-( phi + 180 ))) ] }
I change the value of X from 1 down to 0, say 0.9, 0.8,.....
that means i completely change the orientation of the bond.
Now, my problem is how can i implement this special term in gromacs
code only for my particular dihedral atoms say B-C (bonded atoms
A-B-C-D) with simulation continues as usual normally for all other
bonds.
Please do not mind for sending mail to you personally.
looking forward for your answer.
Thank you very much!
Best regards
Prasad
Message: 9
Date: Wed, 13 Dec 2006 15:54:28 -0500
From: [EMAIL PROTECTED]
Subject: [gmx-users] How to implement dihedral restraints
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
For example, my peptide is rotating 50 degrees about a bond B-C, out of four
bonded atoms A-B-C-D. I want to apply additional force on this
dihedral(B-C) during my simulation(only for this particular atoms to make it
rotate further till 180 degrees). All the remaining atoms in the peptide
will have normal force as usual.
May I ask you, how can I apply this in gromacs code.
Any help will be appreciated!
The current manual is good at describing what the options do for
dihedral restraints, but (to my knowlegde) doesn't explain at all how
to get the implementation up and running. Here is how I have done it
based on searching the mailing list for answers. I suggest that
something like this is added by way of example to the manual for
future releases.
Also, the manual is a bit unclear about whether this type of dihedral
restraint is stable for use near 180deg. I have found that for my
system everything appears to behave normally and as expected over the
entire range of dihedral angles including 180deg.
In your .top file:
; Include forcefield parameters
#include "ffoplsaa.itp"
; Include topologies
#include "myprotein.itp"
[ dihedral_restraints ]
; ai aj ak al type label phi dphi kfac power
A B C D 1 1 180 0 1 2
#include "tip4p.itp"
etc...
Make sure that the dihedral_restraints section comes immediately after
the inclusion of the protein topology. If you have the protein
topology directly in your .top file then just include
dihedral_restraints after the protein listing but before any mention
of things that are not that protein molecule.
Add this to your .mdp
;dihedral restraints
dihre = simple
dihre_fc = 100 ; or whatever value you desire
dihre_tau = 0.0
nstdihreout = 50
For more information about what these options mean, please refer to
the manual.
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