[gmx-users] dihedral MM scan

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Thu Jan 26 06:30:33 CET 2017

Regarding the CGenFF article by Vanommeslaeghe et al. (2009):

It is mentioned that:

"... are correlated, as are their parameters. In such cases, the individual
dihedrals are still scanned at the QM level with all other degrees of
freedom, including other dihedrals that have to be fit allowed to relax.
However, when scanning the corresponding MM surfaces for a given dihedral *it
is necessary* that the remaining dihedrals associated with parameters that
are being fit *be restrained in the QM optimized structures from the QM PES*.
The use of these additional restraints assures that the energy
contributions from those dihedrals are taken into account when performing
the fitting" (Vanommeslaeghe et al. (2009))

When I did the MM scanning, I ignored the other associated dihedrals (some
of them were highly correlated) which are in their local minima in QM
scanning. However, I did an EM step with a tolerance of 50 and I assumed
that those associated dihedrals will go into their local minima which
should be similar with QM case.

If I understood correctly from this article, I should use exactly the QM
optimized structure for each specific angle, and apply restraints to all of
them (except the one that I am trying to scan) during zero-step MD energy
calculation. That being said, taking the structure from that and
restraining, I do not need the EM step by MM force field any more. Is this

Thanks in advance for your opinion

On Wed, Jan 25, 2017 at 10:14 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Hi Justin,
> I did a dihedral population analysis in both bilayer and HII phase.
> Interestingly, the population analysis is consistent with the QM profile
> from GAAMP.  (i.e. I see more population in deeper local minima in QM
> profile, and the population is 0 at QM barriers)
> There is only one exception, though. and it is when the Nitrogen atom is
> protonated (there is a (CH2)-(CH2)-(N)-2(CH3) group at the top part of
> lipid head group),
> If I do a dihedral population analysis in vacuum, it matches the QM
> profile pretty reasonable.
> However, if I use this cationic lipid in a system (either bilayer or HII
> phase), the population profile changes significantly (I mean the shape
> change completely).
> This one is not consistent with QM profile. I think this might be because
> of strong interaction with PS lipids which are negatively charged.
> So, I have made a mistake in my MM scan. I will check it again to see what
> is the problem. Based on these analysis I expect to get quite good MM PES
> profiles.
> Cheers
> Mohsen
> On Tue, Jan 24, 2017 at 1:48 PM, Mohsen Ramezanpour <
> ramezanpour.mohsen at gmail.com> wrote:
>> Hi Justin,
>> Sorry, I am just doing some dihedral population analysis to see which
>> part is wrong.
>> I agree. Most likely I am making some mistakes which is hidden to my
>> eyes. I will prepare and share those with you with the result of population
>> analysis when prepared.
>> Cheers
>> Mohsen
>> On Thu, Jan 19, 2017 at 7:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>> On 1/19/17 9:40 PM, Mohsen Ramezanpour wrote:
>>>> Thanks Justin,
>>>> I did the scan for the whole range from -180 to 180 in 10 intervals.
>>>> I used emtol = 50, and restrain force of 100000 to have a better
>>>> relaxation
>>>> and restraining, respectively.
>>>> Unfortunately, my MM profiles do not look similar to GAAMP QM or MM
>>>> profiles, although I have used the suggested parameters.
>>>> To check the method I am using and the parameters in the .mdp files, I
>>>> did
>>>> the MM scanning on a rotatable bond (CH2-CH2-CH2-CH3) similar to one
>>>> can be
>>>> found in a lipid tail.
>>>> This dihedral was detected as a soft dihedral by GAAMP and there was a
>>>> good
>>>> agreement between QM and MM profiles.
>>>> Here again, my MM profile from scanning does not seem reasonable.
>>>> Most importantly, there is a very large barrier at angle 0 (ca. 300
>>>> times
>>>> of energies in other angles). Besides, there are sudden increase or
>>>> decrease in energy just by 10 degree of rotation.
>>>> Any suggestion is appreciated in advance.
>>> There's really nothing I can suggest without actually seeing the files
>>> (plots of the energy, the QM inputs and your topology).  Something is
>>> inconsistent but it's not clear what.
>>> -Justin
>>> --
>>> ==================================================
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>> ==================================================
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