[gmx-users] Simulation of polarizable Carbon nanotubes

[Justin Lemkul]

On 6/29/15 1:56 PM, S.M. Golam Mortuza wrote:
> Hi Justin,
> Thank you so much for your suggestion. Also, thanks a lot for taking a close look at the paper. I've contacted with the authors of the paper and asked the topology. In the mean time, I've tried simulating a system of a benzene using the method described in the paper, and it ran successfully. So, I am assuming it's the problem with the value of polarization for carbon nanotube.
>

Good to hear!

> Anyway, I've compiled the new code as per your suggestion. I am just wondering whether it's possible to merge this new code with the previous version of gromacs, which is already installed in my computer. Or, are they two different executables and need to be run separately based on my preference? If the latter case, what is the executable names for the new code. For instance, we use grompp, mdrun, etc. for the regular version of gromacs. Are they similar for the new code as well?
> Please accept my apology if these are very dumb questions. Actually, I am not understanding which executables need to be used for the new code to run a simulation, since I do not see the common executables of gromacs (e.g., grompp, mdrun, etc.) after I installed the new code. Any help would be highly appreciated.

You can't merge the new code with old executables.  You simply have to install 
the new code and use it.  The new GROMACS convention is a single binary called 
"gmx" and everything else is called as a module of it.  So instead of "grompp" 
you now have "gmx grompp" and "mdrun" is "gmx mdrun," etc.  Functionally there 
is no difference, it's just a new syntax.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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