[gmx-users] nitrogen itp file with virtual site
Justin Lemkul
jalemkul at vt.edu
Wed Jul 19 15:50:34 CEST 2017
On 7/19/17 9:48 AM, Ali Ahmed wrote:
> 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
You're missing several required directives. Start by reading Chapter 5 of the
manual and the associated tables that show you the order in which things have to
appear. Google can also help - the answers are all out there in the archive :)
-Justin
> --------------------------------------------------------
> 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
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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
>>>>>>
>>>>>> ==================================================
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>>>>>> Gromacs Users mailing list
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>>>>>> * 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
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
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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
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> send a mail to gmx-users-request at gromacs.org.
>>
--
==================================================
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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