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:
[God]
21 22
[Bad]
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
be fine.
-Justin
I hope what I said is clear to you all and I really appreciate your any
suggestions.
Yang
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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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