[gmx-users] about the bond connection between different groups
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 22 03:58:24 CEST 2009
He, Yang wrote:
> Hi Justin,
> It seems that I can not fix the fragmentation fault when position restraints
> is added and hence, I just consider using the freezegroup method to make some
If all trials of PR fail, even test cases with known systems, then you need to
consider that your installation of Gromacs is faulty. All you posted before was
that you have version 3.3.1 on Linux, with no mention of compilers, hardware, or
what Linux distro you use. All of this is important information in diagnosing
Another option is to use a more modern version of Gromacs (4.0.4 is the most
current), and see if the issue is resolved.
> atoms in a whole group fixed .While the freezegroup seems to just be useful
> for the whole group not applicable to some certain atoms in a whole group, I
> consider defining the atoms I want to fix as an individual group and keep the
> other atoms in a nother group but still the fixed atoms are connected to
> another group because of the bond connection. Hence, I just wonder whether I
> can connect the atoms from different groups like that.
In principle, this should work fine. You posted an error before that comes from
the topology, which should not be related to freezegrps. I can tell you that
having multiple freezegrps works fine, even if they are bonded to each other.
There is really no reason to separate these groups, they can be merged into one,
unless you are freezing them in different directions.
> You have said bonds between distinct molecules require a merged topology. Is
> there any introduction in the manual or Do you have any example about the
> merged topology?
A merged topology contains multiple moleculetype definitions in one topol.top.
Discussions are in the archives.
> Thank you for your reply .
> Yang ________________________________________ From:
> gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of
> Justin A. Lemkul [jalemkul at vt.edu] Sent: Tuesday, April 21, 2009 5:49 PM To:
> Discussion list for GROMACS users Subject: Re: [gmx-users] about the bond
> connection between different groups
> He, Yang wrote:
>> Hi all users,
>> I wonder whether it is allowed to define the bond connection between
>> different group in gromacs. Suppose atom A is in group1 and there is
>> another atom B in group2 .Then, I want to define bond between atom A and B.
>> I am not sure whether this is available in gromcas.
> You'll have to elaborate on what you want to do. Bonds are easily defined
> within the topology. Bonds between distinct molecules require a merged
> topology, which is a bit more complicated.
>> Thank you for any suggestions about that.
>> Yang _______________________________________________ gmx-users mailing list
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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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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