[gmx-users] Force constant, regarding

Dallas Warren dallas.warren at monash.edu
Sat Sep 15 04:52:32 CEST 2018

Read the papers for the forcefield, that will tell you how things are

On Sat, 15 Sep. 2018, 2:49 am RAHUL SURESH, <drrahulsuresh at gmail.com> wrote:

> Hi Users
> I am performing a simulation for a bonded metal-protein complex system.
> Here I am aware of adding the essential parameters in ffbonded .itp. The
> force constant value (kb) in the ffbonded.itp file is calculated using
> Gaussian. I would like to clarify the method I have adopted to measure kb
> value.
> Here the metal is bonded with three residues of a protein. I have isolated
> the metal-bonded residue and optimized using gaussian calculated the Kb
> value. Now in ffbonded.itp file, I have added Metal and residue atom bond
> length and  Kb value obtained from QM results, just like
> CU   O    0.20134   507545.
> likewise, I have added all the bonds but kb remain the same.
> Regarding bond angle and dihedral, if the metal is bonded with oxygen of
> two histidines, what should be the nomenclature in naming atoms. Naming can
> be our choice or does it need to follow any protocol?
> How to calculate the cth value for the bond angle?
> How do we determine the coefficients of dihedral?
> Do I make the procedure complicated or can anyone suggest if any better
> methods?
> Sorry I have dumped the mail with too many questions.
> --
> *Regards,*
> *Rahul *
> --
> 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