[gmx-users] about the bond connection between different groups

[He, Yang]

Hi Tsjerk,

Thank you for your reply. SO you mean I can just define the bond in one moleculetype.As what you said, I have to renumber all atoms from one of the moleculetypes,
starting at N+1, with N being the number of the last atom of the first moleculetype .Then I wonder  which molecule type the atom N+1 belongs to . Also, I wonder how to define the new atom N+1's moleculetype  in the gro file . I just am not sure about that. Can you give me much more information about that?

Thank you very much.

Yang
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Tsjerk Wassenaar [tsjerkw at gmail.com]
Sent: Tuesday, April 21, 2009 11:22 PM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] about the bond connection between different groups

Hi He Yang, Justin,

>> 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.

Bonds can only be defined within moleculetypes, not between them. So
you'll need to combine moleculetypes to create a bond between groups.
For this you have to renumber all atoms from one of the moleculetypes,
starting at N+1, with N being the number of the last atom of the first
moleculetype. You also have to renumber the indices for all other
blocks ([bonds], [angles], etc...). Then combine the blocks and
finally add the new bond. If it is a proper bond, you should also
consider adding the angles and dihedrals involved in the interaction.
Note again, merging to create a bond does not mean adding multiple
moleculetypes in one topol.top!

Cheers,

Tsjerk

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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