[gmx-users] large number of molecules

[Justin A. Lemkul]

ksm tprk wrote:
> Yes I was using ffgmx. I tried to use oplsaa but it didn't work. I am 
> using gromacs 3.3.1 and it looks like it doesn't have n2t file beside ffgmx.
> How can i use oplsaa in gromacs 3.3.1
> 

I would suggest at least solving one problem at a time.  If your procedure is 
fundamentally flawed, then it will fail regardless of the force field.  You've 
yet to respond to my comments, and I think that your thermostatting is 
potentially very problematic.

If you want to use OPLS, you'll likely have to write your own .n2t file.  This 
has been discussed in the list archive several times, I believe in the specific 
case of CNT's.  At the very least, the file format is described on the Gromacs 
site and examples are in the archive.

-Justin

-- 
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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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