[gmx-users] Fw: Simulation of polarizable Carbon nanotubes

[Justin Lemkul]

On 7/8/15 4:57 PM, S.M. Golam Mortuza wrote:

This is the problem:

> [ bonds ]
> 1       2       1   0.09572     458148.
> 1       3       1   0.09572     458148.
>
> [ angles ]
> ; i     j       k
> 2       1       3    1   104.52     417.6
>

SWM4-NDP is a rigid water model.  You should not be using flexible bonds and 
angles.  Remove this section and replace with

[ settles ]
; i   j funct   length
1     1 0.09572 0.15139

The run proceeds fine with proper rigid treatment of the water.

-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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