[gmx-users] nitrogen itp file with virtual site
Ali Ahmed
aa5635737 at gmail.com
Mon Jul 17 21:39:33 CEST 2017
Dear Justin
Here is the topology file I wrote. I included all the parameters rather
than use a specific FF.
Thank you for your support
..
-------------------------------------------------------------------------------------------------------------------------
; virtual sites have zero mass which leads to zero Moment of inertia
;virual sites have charge only 0.482 e. to balance the nitrogen atom
negative charge -0.482 e.
; the distance between two nitrogn atoms N--N is 0.11 nm
;the distance between two virtual sites is 0.15 nm
;the distance between nitrogen atom and virtual site is 0.02 nm. This makes
the virtual site attached to the nitrogen atom
;
[ atomtypes ]
; name bond_type mass charge ptype sigma epsilon
N N 0.000 0.000 A
0.332 0.3026
MN MN 0.000 0.000 A 0.000
0.000 ; MN is the virtual sites
[ moleculetype ]
; name nrexcl
N_2 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 N 1 N_2 N1 1 -0.482
14.0067
2 N 1 N_2 N2 1 -0.482
14.0067
3 MN 1 N_2 M1 1 0.482
0.0000
4 MN 1 N_2 M2 1 0.482 0.0000
[ constraints ]
; There are no bonds in this system
; Instead, we fix the distance between the mass centers such that
; the virtual sites can be reconstructed
3 4 1 0.15
[ system ]
CO2 in vacuo
[ molecules ]
N_2 30
On Mon, Jul 17, 2017 at 12:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> 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
>>>
>>> ==================================================
>>> --
>>> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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