[gmx-users] Error in simulating graphene

[Justin Lemkul]

On 7/13/17 5:49 AM, B S Bhushan wrote:
> Dear Experts,
> 
> I am new to gromacs. I want to simulate electric double layer capacitance
> at graphene - liquid electrolyte interface. so far, I have practiced the
> tutorials from bevanlab page "Lysozyme in water" "biphasic systems". Next,
> I was trying to simulate the CNT/graphene tutorials available at thirdparty
> web pages. How ever I am getting errors while trying to generate topology
> file using *x2top* module.
> 
> When following the tutorial given at
> http://chembytes.wikidot.com/grocnt#toc
> I am getting the error,
> "*Inconsistency in user input:*
> *Could not find force field 'cnt_oplsaa' in current directory, install tree
> or*
> *GMXLIB path*."
> 

This means the force field isn't anywhere the the program can find it.

> 
> When following the tutorial given at
> http://machine-phase.blogspot.in/2009/04/single-wall-carbon-nanotubes-in-403.html
> I am getting the error,
> "*Fatal error:*
> *Could only find a forcefield type for 0 out of 168 atoms.*"
> 

The .n2t file is constructed incorrectly such that no topology assignments can 
be made.

-Justin

-- 
==================================================

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

==================================================