[gmx-users] nitrogen itp file with virtual site
Ali Ahmed
aa5635737 at gmail.com
Wed Jul 19 15:48:12 CEST 2017
Dear Justin
I have checked and tried but still not working, it says ( invalid order for
directive atomtypes). Please can you take a look on the following
--------------------------------------------------------
Here is the topology file
;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 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
M M 0.000 0.000 V 0.000
0.000 ;
[ 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 M 1 N_2 M1 1 0.482 0.0000 ; MN
is the virtual site
4 M 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
1 2 1 0.11
[ system ]
Nitrogen in vacuo
[ molecules ]
N_2 1000
-----------------------------------------------------------------------------------------------------
here is the pdb file
TITLE N_2 with dummy masses
REMARK THIS IS A SIMULATION BOX
CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 N1 N_2 1 0.000 0.000 0.000 1.00 0.00
ATOM 2 N2 N_2 1 1.100 0.000 0.000 1.00 0.00
ATOM 3 M1 N_2 1 0.200 0.000 0.000 1.00 0.00
ATOM 4 M2 N_2 1 0.900 0.000 0.000 1.00 0.00
TER
ENDMDL
-----------
Thank you
On Tue, Jul 18, 2017 at 8:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/17/17 3:39 PM, Ali Ahmed wrote:
>
>> 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
>>
>>
> This is incorrect; the virtual site should be particle type V, not A.
>
>
>>
>> [ 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
>>
>>
> This is why your system is failing. You're defining a constraint between
> the virtual sites and no bonded interaction at all between the N atoms. If
> the N-N bond is to be constant at 0.11 nm, then set it as a constraint
> (between atoms 1 and 2) and construct the virtual sites based on the real
> atoms in the system.
>
> -Justin
>
>
> [ 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
>>>>>>>
>>>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>>>> or
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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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>>>>>
>>>>>
>>>>> --
>>> ==================================================
>>>
>>> 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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>>>
>>>
> --
> ==================================================
>
> 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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>
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>
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