[gmx-users] colour of the molecules

[Justin A. Lemkul]

hhhh huan wrote:
> Dear all gmx-users and developers,
> 
> There are 6 different type of molecules in my simulation system. So how can I differentiate o recognize the type of those molecules? which files (topology, trr or others) should I look at? 

If this is a simple visualization issue, it can be taken care of within (for 
example) VMD.  Each residue in your system should have a unique residue number 
(or for each molecule, if they are separate entities).

You can use "resid 1" and a ColorID designator in VMD to illustrate just 
molecule/residue 1.

All of this information comes from the structure file (.gro/.pdb).

-Justin

> 
> Any suggestions are appreciated.
> Thanks
> 
> 
> 
>       
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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