[gmx-users] nitrogen itp file with virtual site
aa5635737 at gmail.com
Mon Jul 17 17:38:20 CEST 2017
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?
Thank you very much I appreciate your support.
On Mon, Jul 17, 2017 at 8:40 AM, Justin Lemkul <jalemkul at 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
>> (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.
> 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
>> 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
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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