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.
-Justin
Thanks in advance.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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