[gmx-users] Help for using Lincs along with constraint

[Justin Lemkul]

On 2/3/19 10:00 AM, anupama sharma wrote:
> Dear user's
>   I need help for using lincs along with constraint. I am doing water
> (tip4p/2005) and  carbon nanotube simulation and since I am using
> tip4p/2005, I had used exclusion for rigid body dynamics and for that I
> kept lincs off. But after nvt simulation bonds in carbon nanotube is
> getting broken. What I can do for that.....

LINCS is not applied to water unless you are manually defining the 
constraints (e.g. not using SETTLE).

You will have to define what you mean by "getting broken," because that 
may simply be a PBC effect. Bonds are bonds. They don't break in an MD 
simulation. Our ability to perceive them as the physics intends, 
however, is another matter.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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