[gmx-users] Repulsive potential

[Hassan Aaryapour]

Dear Atsutoshi,

Very thanks for your reply. I run repulsive/nonrepulsive potential
simulations for a system contains (Di-peptide + 2Ligand) for 5ns as
suggestions and, compared final results by VMD. I don't think that there is
really difference between two simulation, ligands are aggregated in both
simulation. All necessary results is uploaded as follow:

http://d01.megashares.com/?d01=HrNDcu4

http://d01.megashares.com/?d01=kdLuTf7


 I would greatly appreciate if you could kindly tell your comments and, if
possible share your required file.


 Sincerely

Hassan




On Tue, Jul 21, 2015 at 11:42 AM, <atsutoshi.okabe at takeda.com> wrote:

>  Dear  Hassan,
>
>
>
> I’m sorry for my late reply. I missed your e-mail.
>
>
>
> I think the easiest way to introduce repulsive potential is  to use draft
> code for  inter-molecular bonded interaction at
> https://gerrit.gromacs.org/#/c/2566/. But nobody has yet tried that it
> works as Mark said.
>
> Another way, as Justin told us, is to define a dummy atom within the
> structure using a virtual site, then specifying a nonbonded interaction
> only between these virtual sites using [nonbond_params].
>
> However, I am getting some errors using this methods and trying it if it
> works well.
>
>
>
> Atsutoshi
>
>
>
> *From:* Hassan Aaryapour [mailto:hassan.gromacs at gmail.com]
> *Sent:* Friday, June 26, 2015 7:41 PM
> *To:* Okabe, Atsutoshi
> *Subject:* Repulsive potential
>
>
>
> Dear Atsutoshi Okabe,
>
> I read your email to “mark abraham” about introducing weak repulsive
> potential. I have this problem and, don't know how to do it. I would
> greatly appreciate if you could share your experience and, help me do that
> for a simulation system contains Protein + 6Ligands + Ions and waters
> molecule.
>
> Best Wishes
>
> Hassan
>