On 7/17/17 11:38 AM, Ali Ahmed wrote:
Dear Justin
Thank you very much. As I saw in some literature (as in the link below)
that N atom has a negative charge and needs a massless positive charge. I
tried with most of the FFs but could not produce nitrogen density above
critical point. I don'n know which FF is the best one and I'm new to MD
simulations and new GROMACS user.
Could you please tell me which FF should I use?
What you're citing is a custom model. You can write the force field files very
easily. I see what you're trying to do now, but you should be clear that N2 is
not a negatively charged molecule simply because the N atoms (in this
representation) have partial negative charges. The virtual site balances it out
so that electrostatic properties are better represented.
The virtual site you need to create is a simple one, placed at the center of the
N-N bond, so this is virtual_sites2 with an "a" value of 0.5.
-Justin
Thank you very much I appreciate your support.
http://iopscience.iop.org/article/10.1088/0965-0393/24/4/045002/meta
On Mon, Jul 17, 2017 at 8:40 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 7/16/17 9:20 PM, Ali Ahmed wrote:
Hello GROMACS users,
This is Ali, I'm new to Gromacs and doing MD simulation of nitrogen at
super critical point.The structure I use is different from regular
nitrogen
(N-N). As you know N atom has a negative charge which means the nitrogen
molecule will be negatively charged, therefore I need to use massless and
This is incorrect - N2 carries no formal charge.
charged virtual site to equilibrate the molecule. I have looked on the
tutorial about CO2 to produce the XXX.itp but didnot work with me. Could
anyone have done it before tell me how to do it ?
You don't need virtual sites for a diatomic molecule.
-Justin
Here are the parameters:
N :mass =14.0067, epsilon =(0.3026 KJ/mol), sigma =(0.332 nm), Charge
=(-0.482 e).
XX (massless, charged particle ):mass =0, epsilon=0, sigma=0 Charge= 0.964
e.
Thank you very much.
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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