RE: torsion scan

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Apr 19 2018 - 18:49:48 CDT

Hi Stefano,

Colvars or perhaps extrabonds seem like the easiest ways of implementing what you want, with the advantage of colvars being that you can use the targetNumStages keyword to do half of your scan in one configuration file. You'd just need a giant force constant for the dihedral, since NAMD doesn't know how to SHAKE/RATTLE/SETTLE a collective variable yet.

-Josh

On 2018-04-19 17:36:18-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Dear namd users,
I would like to perform a QM/MM torsion scan with NAMD/ORCA: which strategy could be advisable? Would it be feasible to use colvars module (something like a moving restraint eventually with umbrella sampling) or targeted molecular dynamics?

Thanks in advance
Stefano

--
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178

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