He, Yang wrote:
Hi Justin,
In fact, I have tried to use freezegrps to freeze a whole single CG DNA strand
and it works but if I want to freeze some atoms in this single strand, it seems
that I have no choice but choose the position restraints. The freezegrps seems
not to work for that. But the error for the position restraints always is
fragmentation fault and can not be fixed although many methods have been tried.
So then the following is true:
freezegrps = DNA works fine
freezegrps = (your groups) gives "Invalid order for directive defaults"
That would make no sense. The error comes from the topology, not anything
specified in the .mdp file, so I don't understand.
I don't know whether this is a bug in the gromacs cause I have followed the
steps in manual to simulate a case(about speptide) in manual with position
restraints while it still doesn't work. I am confused about that.
I doubt it is a bug; this would be pretty prohibitory for most users. It may be
specific to your system. If you can provide details of your system, compilers,
which Gromacs version you are using (provided in a new thread that has a
noticeable subject line), you may be able to sort that issue out.
-Justin
Yang
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Sunday, April 19, 2009 4:41 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] (no subject)
He, Yang wrote:
It always show the common error "Invalid order for directive defaults".I suppose it
is because I have defined an atom belonging to two groups . What do you mean "by
freezing subgroups of atoms
within a molecule" ? I just wonder how to make it ?Can you give me some
examples?
The error is unrelated to your freezegrps. See here:
http://wiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults
Your index groups should be fine. A "subgroup" refers to select atoms within a
molecule, as in backbone of the protein, headgroups of lipids, or some such
similar idea. As I said before, your use of freezegrps and index groups should,
in theory, be fine.
-Justin
Thank you very much.
Yang
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Sunday, April 19, 2009 3:47 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] (no subject)
He, Yang wrote:
Hi Justin,
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.
Alright, so what's the error? You should be able to freeze subgroups of atoms
within a molecule; I've done it several times in different instances.
-Justin
Yang
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@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:
[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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--
========================================
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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--
========================================
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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--
========================================
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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