# [gmx-users] g_dipoles

Nilesh Dhumal ndhumal at andrew.cmu.edu
Sun May 11 02:18:48 CEST 2014

```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.

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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```