[gmx-users] Re: Re : Protein carbohydrate simulation

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 20 19:43:43 CET 2010

Contrary to what was advertised on the list, I am not willing to provide 
personal help service to anyone who asks.  Please keep all posts on the list. 
Conversations there benefit the community as a whole.

bharat gupta wrote:
> Hi Sir
> I know how to do the basic simulation and I have done the Lysozyme
> tutorial also . I have a doubt in that also .. like if I am running my
> simulation for say 3ns and I want the structure after every 1 ns ..
> how can I get that ..

trjconv -dump

> And also regarding the parametrization stuff I have got a paper where
> they have improved the OPLS AA force field for carbohydates .. Now how
> to parametrize that new version in the OPLS AA Force Field given in
> GROMACS .. I dont know how to do that ..

Follow whatever protocols are documented in the literature.  Usually some sort 
of charge calculation (ab initio or otherwise) is used, followed by empirical 
fitting to reproduce condensed phase properties.  Details should be given in the 
paper(s) for the parameter set(s).


> If you can help me then pls do reply .....


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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