[gmx-users] dihedral MM scan

[Mohsen Ramezanpour]

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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