[gmx-users] typeB in FEP calculations

[Billy Williams-Noonan]

Hi there,

Because the bond and angle parameters are harmonic terms in many
forcefields, my understanding is that they should cancel out during a
closed thermodynamic cycle.  So you will not need state B parameters for
those terms.

However, you will need to state state B terms for proper and improper
dihedrals though.

Refer to the papers by Boresch, et al. from 1999.

Cheers,

Billy

On 27 September 2016 at 03:34, Rui Neves <rppneves at gmail.com> wrote:

> Hi Gromacs users,
>
> I am trying to determine a relative binding free-energy of two hypothetical
> ligands (A -> B).
>
> To do this, I must indicate a typeB for the atomtypes in B.
> Once this is done, do I have to explicitly include the bonded parameters
> for the B state, if I started by loading all the parameters of the force
> field that parameterizes both ligands?
>
> Thank you for any help,
>
> Regards,
>
> Rui Neves
> --
> 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.
>



-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052