[gmx-users] Gromacs query for vaccum medium

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 4 19:30:27 CET 2011

Anushree Tripathi wrote:
> I have seen different articles on MD simulation in vaccum but i didn't 
> get the exact way for it.If u can tell me the exact way then i can 
> proceed for it fastly because I have to do it within certain time limit.

It would be useful if you were to describe what it is that you're trying to 
replicate, why you don't understand how to do it, and what you have tried. 
Implying urgency or time limits is not appropriate; we all have things that 
we're working on and we're all trying to make progress on our own projects (and 
some of us are nearing completion on dissertations).  The contributors to this 
list take time to offer free advice when they can.  They can do so effectively 
and efficiently with a clear statement of goals and specific questions.


> On Thu, Nov 3, 2011 at 11:43 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 4/11/2011 4:58 AM, Anushree Tripathi wrote:
>         Let me know how to simulate a membrane protein in vaccum medium
>         by using gromacs commands.What are the basic differences in
>         commands as well as parameters used in liquid and vaccum medium?
>         Please guide me.
>     I suggest you do all the GROMACS tutorial material you can find, and
>     supplement that with reading several published articles that do
>     simulations with objectives similar to yours.
>     Mark
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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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