[gmx-users] nitrogen itp file with virtual site

[Justin Lemkul]

On 7/17/17 12:31 PM, Ali Ahmed wrote:
> Dear Justin
> I have tried same what you have said. I followed the tutorial for CO2 but
> didn't work, gave an error during the energy minimization . I'm not sure
> what was the wrong, I noticed the N atoms (in the box) were separated from
> the virtual site after the error.
> 

If you have just N2 in a box in vacuo, then this would suggest a topology 
problem.  Please post the exact text of your .itp file.  It should be quite 
short and easy to spot any problems.

-Justin

> 
> On Mon, Jul 17, 2017 at 10:41 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
>>
>>
>> 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 <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
>>>>> 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
>>>>
>>>> jalemkul at 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
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>> Gromacs Users mailing list
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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

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