[gmx-users] g_dipoles
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Sun May 11 15:31:22 CEST 2014
> On 2014-05-11 02:18, Nilesh Dhumal wrote:
>> I run g_dipoles for two ionic liquids : 1-Ethyl-3-methylimidazolium
>> chloride and 1-Ethyl-3-methylimidazolium ethylsulfate. In both the
>> systems
>> cation is common 1-Ethyl-3-methylimidazolium.
>
>
> I didn't follow the discussion but you can not use dipole moment
> fluctuations to compute the dielectric constant for ionic species as
> every ion that moves to the other side of the periodic box will increase
> the fluctuations artificially.
I am not calculating the dielectric constant for my system. I am
calculating the dipole moment of the system. For dipole moment calculating
program put the periodic boundary condition off. I calculated the dipole
moment for two different systems. In one system program calculate the
total charge on residue and change is 1. Program will subtract their
charge at their center of mass for one system and for other system it
don't do. Both the system have cation and anion. Why program is not
following same protocol for both systems? Why program is subtracting atom
charges at their center of mass for dipole moment calculation.
Nilesh
>
>>
>> In g_dipoles comde
>>
>> static void neutralize_mols(int n,int *index,t_block *mols,t_atom *atom)
>> {
>> double mtot,qtot;
>> int ncharged,m,a0,a1,a;
>>
>> ncharged = 0;
>> for(m=0; m<n; m++) {
>> a0 = mols->index[index[m]];
>> a1 = mols->index[index[m]+1];
>> mtot = 0;
>> qtot = 0;
>> for(a=a0; a<a1; a++) {
>> mtot += atom[a].m;
>> qtot += atom[a].q;
>> }
>> /* This check is only for the count print */
>> if (fabs(qtot) > 0.01)
>> ncharged++;
>> if (mtot > 0)
>> /* Remove the net charge at the center of mass */
>> for(a=a0; a<a1; a++)
>> atom[a].q -= qtot*atom[a].m/mtot;
>> }
>> }
>>
>> if (ncharged)
>> printf("There are %d charged molecules in the selection,\n"
>> "will subtract their charge at their center of
>> mass\n",ncharged);
>> }
>>
>>
>>
>> For 1-Ethyl-3-methylimidazolium chloride, program don't print "There are
>> %d charged molecules in the selection will subtract their charge at
>> their
>> center of " and for other ionic liquids it do.
>> For 1-Ethyl-3-methylimidazolium ethylsulfate ionic liquid program show
>> the
>> comment and recalculate the charges.
>>
>> /* Remove the net charge at the center of mass */
>> for(a=a0; a<a1; a++)
>> atom[a].q -= qtot*atom[a].m/mtot;
>> }
>>
>> I don't know why program is not using same protocol for all system.
>>
>> What could be the reason to remove the net charge at the center of mass
>> for dipole moment calculation.
>>
>> Nilesh
>>
>>
>>
>>>
>>> On 4/27/14, 4:33 PM, Nilesh Dhumal wrote:
>>>>>
>>>>>
>>>>> On 4/27/14, 4:25 PM, Nilesh Dhumal wrote:
>>>>>>>
>>>>>>> On 4/27/14, 4:01 PM, Nilesh Dhumal wrote:
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I run g_dipoles for two different systems (System are ionic
>>>>>>>> liquids).
>>>>>>>>
>>>>>>>> For one system when I run g_dipoles I get following message
>>>>>>>>
>>>>>>>> There are 256 molecules in the selection
>>>>>>>> There are 256 charged molecules in the selection,
>>>>>>>> will subtract their charge at their center of mass
>>>>>>>>
>>>>>>>>
>>>>>>>> and I don't get this message for other system.
>>>>>>>>
>>>>>>>> Why program subtract their charge at their center of mass for one
>>>>>>>> system
>>>>>>>> and not for other.
>>>>>>>>
>>>>>>>
>>>>>>> Based on whatever the topology says, g_dipoles doesn't find a net
>>>>>>> charge
>>>>>>> on
>>>>>>> whatever these molecules are. Without providing more information -
>>>>>>> what
>>>>>>> the
>>>>>>> molecules/selections are, what the topology(ies) is(are) - that's
>>>>>>> all
>>>>>>> that
>>>>>>> can
>>>>>>> be surmised at this point.
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>
>>>>>> There are 128 cations (EMI) and 128 anions (ETS). Total charge is
>>>>>> ZERO
>>>>>>
>>>>>> here is molecular section from topology file.
>>>>>> [ defaults ]
>>>>>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>>>>>> 1 3 yes 0.5 0.5
>>>>>>
>>>>>> #include "emi.itp"
>>>>>> #include "ets.itp"
>>>>>>
>>>>>>
>>>>>> [ molecules ]
>>>>>> ; Compound #mols
>>>>>> EMI 128
>>>>>> ETS 128
>>>>>>
>>>>
>>>> For other system I have different anion. I didn't specify the number
>>>> of
>>>> residues in molecular section.
>>>>
>>>> [ system ]
>>>> ; Name
>>>> Grunge ROck MAChoS t= 20000.00000
>>>>
>>>> [ molecules ]
>>>> ; Compound #mols
>>>> Ion 1
>>>>
>>>
>>> So "Ion" is some collection of molecules, or what? If it's a single
>>> [moleculetype] composed of multiple molecules, each bearing a net
>>> charge
>>> but
>>> adding up to zero for the whole [moleculetype], this explains your
>>> observation.
>>> g_dipoles reads "Ion" as being a neutral entity, which is probably
>>> not
>>> correct
>>> for a program like g_dipoles.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> 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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>>
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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