[gmx-users] colour of the molecules

[Justin A. Lemkul]

hhhh huan wrote:
> Dear all gmx-users and developers,
>  The simulation has been carried out and I cant recognize the type of molecule since there are 6 different type of mlecules in that system.
> thanks.

I know I'm still a bit lost as to what the problem is.  You've conducted a 
simulation, but you don't know what's in the system?  Look in the output .gro 
file for molecule names.  The .top file will have atom types and such.

If this is a visualization problem, have you tried what I suggested to you earlier?

http://www.gromacs.org/pipermail/gmx-users/2008-August/035723.html

-Justin

> 
> 
> --- On Wed, 8/13/08, Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de> wrote:
> 
>> From: Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de>
>> Subject: Re: [gmx-users] colour of the molecules
>> To: scottiehuan at yahoo.com, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Date: Wednesday, August 13, 2008, 2:28 PM
>> Hi,
>>
>> On Wednesday, 13. August 2008, 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?
>>>
>>> Any suggestions are appreciated.
>>> Thanks
>> please describe your problem with more details, have you
>> setup a simulation?
>>
>>
>>>
>>>
>>>
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>>
>> greetings,
>>
>> Florian
>>
>> -- 
>> -------------------------------------------------------------------------------
>>  Florian Haberl                        
>>  Computer-Chemie-Centrum   
>>  Universitaet Erlangen/ Nuernberg
>>  Naegelsbachstr 25
>>  D-91052 Erlangen
>>  Telephone:  	+49(0) − 9131 − 85 26573
>>  Mailto: florian.haberl AT chemie.uni-erlangen.de
>> -------------------------------------------------------------------------------
> 
> 
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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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