[gmx-users] linear molecules

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 5 19:01:13 CEST 2010

nadia teresa de la cruz canul perez wrote:
> Hi,
> I want to simulate a system of linear molecules like CO2 with periodic 
> boundary conditions. I think this can be done with the
> virtual sites algorithm. I have started with GROMACS today. Do you have 
> some sample scripts for linear molecules which use
> the virtual site algorithm which could help me? I have  read that I need 
> topology files but I dont know how to generate them for virtual sites.

The manual should be your first resource, since that is where topologies and 
virtual site definitions are discussed.  Then check the mailing list archive. 
You are not the first person to attempt to build CO2, and there are certainly 
many other examples of linear molecules that others have attempted.


> Thanks in advance.


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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