VMD-L Mailing List

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Wed Aug 09 2017 - 15:22:53 CDT

Hi Ms. Malik,

Thanks very much for your reply. Actually I want to find out pairs of atom
which are having electrostatic interaction in a protein-lipid system.
Actually, I have output from the hbonds plugin which shows me donor and
acceptor of all hydrogen bonds that formed during a specified time of
simulation and their occupancy. But there are electrostatic forces other
than only hydrogen bonds like ionic bonds, dipole-dipole, dipole-induced
dipole etc bonds. I am wondering if there is any way to find out atom pair
which are having electrostatic interaction and the occupancy during the
simulation.

Hope I can explain what I am looking for.

Regards
Rabeta Yeasmin

On Wed, Aug 9, 2017 at 2:27 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> Electrostatic interactions are charge dependant. Any two things that will
> have a charge will interact.
>
> You need to decide what distance you want to use as cutoff and based on
> that calculate interactions between charged particles.
>
> The interactions will be computed as energies. Is that what you are after?
> From the subject it sounds like you are not interested in energies but
> rather the number of hydrogen bonds. Is that the case?
>
> In either case you will have to make selection groups of your atoms and
> then use the NAMD energy plugin for example to calculate the energies
> between those selection. If you want the number of hydrogen bonds you can
> use the hbond plugin for those selection groups.
>
> Hope this helps.
>
> On Aug 10, 2017 6:56 AM, "Rabeta Yeasmin" <rabetayeasmin_at_gmail.com> wrote:
>
>> Dear VMD Users,
>>
>> I want to find out which atoms have electrostatic interaction of a
>> protein-lipid system. I am wondering if you can suggest me how can I do
>> this.
>>
>> Thanks.
>>
>> Regards
>> Rabeta Yeasmin
>>
>