[gmx-users] (no subject)
yang.he at mavs.uta.edu
Mon Apr 20 00:34:46 CEST 2009
In fact, I just get the error. I have tried to use the freezegroup but it seems that it only work for the whole group not certain atoms in the whole group.
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Sunday, April 19, 2009 1:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] (no subject)
He, Yang wrote:
> Hi all users,
> I am trying to create the ndx file to define the atoms which I want to add the position restraints to. What I create is like this:
> 21 22
> 61 62
> And I have defined the atom numbering 21, 22, 61,62 in gro file like this :
> 2MOM bT 21 0.805 1.330 3.914
> 2MOM bT 22 0.448 1.572 3.576
> 4ICE bT 61 0.805 4.330 3.914
> 4ICE bT 62 0.448 4.572 3.576
> I know this may cause error cause I just define one atoms in two groups. I just want to freeze only two atoms in the group[MOM](A single DNA strand) while keep the other atoms in this group move freely , Meanwhile, the two frozen atoms have a bond connection with the other atoms in this [MOM]group ,which is assumed that this single DNA strand will be fixed because of the two fixed atoms and the other atoms will move freely at the same time. I wonder how I can define this position restraints in gromacs .
Are you assuming an error, or have you tried it and actually received an error?
Use these groups as the "freezegrps" in the .mdp file and try it. It should
> I hope what I said is clear to you all and I really appreciate your any suggestions.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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