[gmx-users] Topology file of molecule
krzysztof.kolman at gmail.com
Tue Dec 5 13:11:01 CET 2017
Dear Vytautas and Justin,
Thank you both for the help. I will try to perform some dihedral scans of
small and simple molecules.
2017-12-04 15:24 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> On 12/4/17 5:31 AM, Krzysztof Kolman wrote:
>> Dear Justin,
>> Since you last answer, I have been trying to find some description how to
>> perform dihedrals scans using some QM software and Gromacs. I have found
>> out that it used to be some QM software implemented in Gromacs (Orca) but
>> this implementation is not developed anymore and it does not work with
>> newer version of Gromacs and Orca, please correct me here if I am wrong. I
> The QM/MM interface is not really maintained. This is also not what you
> really should be using. The QM dihedral scans you need to apply have no MM
> component, so you don't need GROMACS at all. In general:
> 1. Perform a QM optimization at a suitable level of theory
> 2. Create a series of input files with systematically varying values of
> the target dihedral, and perform an optimization of the structure with that
> dihedral frozen.
> 3. Compute the potential energy surface of those optimized configurations.
> have been also trying to find out how to do the MM part using Gromacs and I
>> found out that the simulations should have some unusual parameters
>> (cutoffs, etc.) and it is quite tedious work since all the input files
>> to be manually prepared. My question is do you know maybe if there is
>> somewhere a tutorial how to perform such scans using Gromacs where all
>> knowledge is combined and also some semi-automatic solution is presented?
> No, and this is something that is indeed very laborious in GROMACS. You'd
> have to perform a series of optimizations (energy minimizations) with
> dihedral restraints, which have different values (could be easily scripted
> there), and then a single-point energy value computed in the absence of
> restraints. This is trivial to do in a program like CHARMM, it is more
> tedious in GROMACS.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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