[gmx-users] g_dipoles
David van der Spoel
spoel at xray.bmc.uu.se
Sun May 11 14:33:46 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.
>
> 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
>>
>> ==================================================
>> --
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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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