[gmx-users] Creating metal ion dummy models for MD simulations.

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 25 19:20:39 CEST 2017


I suggest you contact the corresponding author of such papers and ask them
to share, since a quick glance at their supporting information did not make
clear to me what they had done.


On Tue, 25 Jul 2017 10:40 Abhishek Acharya <abhi117acharya at gmail.com> wrote:

> Dear Users,
> I want simulate a protein bound to two copper ions. For this, I intend to
> use a dummy model for the metal ions with 6 dummy atoms surrounding each
> metal ion. The parameters will be obtained from the following publication:
> http://pubs.acs.org/doi/10.1021/acs.jpclett.5b01122
> Since, I am new to the use of dummy models in GROMACS, I wanted to know the
> correct way to represent the topology for such models. I tried to look for
> example .itp files but couldn't find one. I went though the gromacs manual,
> especially dummy atoms section (or virtual sites). But, I am pretty sure
> this is not applicable to my problem; virtual sites have no mass, whereas
> the dummy models as described in the above publication have dummy atoms
> with a mass of 3.000 amu. I am guessing that the correct way should be to
> treat the dummy model as a single molecule with 7 atoms, one central metal
> ion and 6 dummy atoms, but i may be wrong.
> Kindly let me know the correct method to represent the topology.
> Alternatively, it would also be a great help if someone can provide itp
> files used in the above study, or any example itp files with similar dummy
> models.
> Also, which software is generally used to construct the coordinates for
> such dummy models ?
> Thanks and Regards,
> Sincerely,
> Abhishek Acharya
> Department of Molecular Nutrition
> CSIR-Central Food Technological Research Institute,
> Mysuru-570020
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list