[gmx-users] g_dipoles

[Nilesh Dhumal]

>
>
> 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

Nilesh

>
> You said you had two different systems.  What's the difference between
> them?
>
> -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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