[gmx-users] g_dipoles

[Justin Lemkul]

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

==================================================