Re: Selective accelerated MD in NAMD

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri Apr 06 2018 - 17:42:15 CDT

Hi Alexander,

I was not aware that you could do accelerated MD on a part of your system.
Could you refer me to the relevant literature?

Chitrak.

On Fri, Apr 6, 2018 at 4:36 PM, Alexander Adams <xadams_at_umich.edu> wrote:

> 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--00000000000096704c056935c440--

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