[gmx-users] Add atom to .itp file

[Justin Lemkul]

On 3/24/14, 5:33 AM, Satyadeep Roat wrote:
> I want to make a new itp file and add two atoms in it.
>
> Something like this
>
> ;[atoms]
>
>
> 1            a1          q      r1
> 2             a2         -q     r2
>

Close, but not correct.  The format for [atoms] is listed in manual section 
5.7.2.  There is no way to specify an atom's radius directly; one needs to use 
LJ parameters that are suitable to define the interaction distances for all the 
atoms.

Also of note here for polarizable systems is that Gromacs calls these particles 
"shells," and they are treated differently from normal atoms, so manual section 
3.5 is relevant here, and the atom type for the shell particle should be chosen 
(or added) such that it is a shell, otherwise there's nothing really polarizable 
about the system; it would just be a system of normal atoms.

-Justin

>
> On Mon, Mar 24, 2014 at 2:47 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> I don't understand your description.
>>
>> Mark
>> On Mar 24, 2014 4:09 AM, "deep" <satyadeep.roat at gmail.com> wrote:
>>
>>> I want to create a polarizable particle system consisting of a sphere
>>> carying
>>> charge q and some size r1 on which a oppositively charge -q is present
>> with
>>> some other size r2 . Overall I want to create a colloidal particle . Can
>>> anyone please help me in making these sphere (atom ) in itp file ? I want
>>> to
>>> write some command and I don't know what exactly I have to write .
>>>
>>> Thanks
>>>
>>> --
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>
>
>

-- 
==================================================

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

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