[gmx-users] dihedral MM scan

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Thu Jan 26 06:15:01 CET 2017

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

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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