[gmx-users] g_dipoles

Justin Lemkul jalemkul at vt.edu
Sun Apr 27 22:29:35 CEST 2014



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
>

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

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


More information about the gromacs.org_gmx-users mailing list