Re: [gmx-users] reg centre of mass in SMD

2011-05-19 Thread Justin A. Lemkul 



vidhya sankar wrote:

Thank you Dr Justinj,
To do SMD should i create centre of mass 
of my reference (protein) and pull group (ligand)? if i  need to create ,

which tool of gromacs generate to be used .?
How to include this center of mass in SMD  .mdp files



None of this is necessary.  Gromacs does all COM calculations internally.

-Justin

--


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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[gmx-users] reg centre of mass in SMD

2011-05-18 Thread vidhya sankar 
Thank you Dr Justinj,
    To do SMD should i create centre of mass of my 
reference (protein) and pull group (ligand)? if i  need to create ,
which tool of gromacs generate to be used .?
How to include this center of mass in SMD  .mdp files

Thanks in Advance

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