[gmx-users] about the bond connection between different groups
yang.he at mavs.uta.edu
Wed Apr 22 03:39:12 CEST 2009
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 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.
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?
Thank you for your reply .
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.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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