Re: Selective accelerated MD in NAMD

From: Alexander Adams (xadams_at_umich.edu)
Date: Fri Apr 06 2018 - 15:36:59 CDT

Hi Eddi,

Thank you for your response. I can choose just to boost the dihedrals of
the system, though literature suggests that this is insufficient to observe
the conformational changes associated with a transport event.

Miao, Y., Nichols, S., Gasper, P., Metger, V. & McCammon, J. Activation and
dynamic network of the M2 muscarinic receptor. Proc. Natl. Acad. Sci. U. S.
A. 110, 10982–10987 (2013).

Ke, M., Yuan, Y., Jiang, X., Yan, N. & Gong, H. Molecular determinants for
the thermodynamic and functional divergence of uniporter GLUT1 and proton
symporter XylE. PLoS Comput. Biol. 1–26 (2017).

On Fri, Apr 6, 2018 at 4:23 PM, Eduard Schreiner <eduard.schreiner_at_gmail.com
> wrote:

> Can't you boost just the dihedrals of the protein?
>
> Eddi
>
> Alexander Adams <xadams_at_umich.edu> schrieb am Fr., 6. Apr. 2018, 21:12:
>
>> Hello all,
>>
>> I am performing a simulation of the transport protein XylE in membrane
>> with the sugar xylose bound in the central pocket. I am using accelerated
>> MD in order to access a conformation change on the nanosecond timescale.
>> Unfortunately, the total potential boost results in the sugar unbinding
>> from the central pocket central pocket and diffusing away from the protein.
>> I know there is a form of aMD in Amber that allows for selective
>> acceleration of just an enzyme, substrate, etc., and was wondering if an
>> equivalent exists in NAMD.
>>
>> Thanks in advance!
>> Alex Adams
>>
>

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