[gmx-users] SMD regarding

[RAHUL SURESH]

THAnk you Dr. Justin

That’s convincing a lot.


On Sat, 12 May 2018 at 8:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/12/18 10:41 AM, RAHUL SURESH wrote:
> > Thank you Dr. Mark
> >
> > Is it valid to do such simulation despite causing the distortion in
> lipids?
>
> Lipids are highly dynamic. They can tilt, flip-flop, pack and expand.
> What you need to do is perform your simulation in such a way that the
> lipids are not *artificially* distorted purely as a consequence of what
> you are doing. Performing the SMD with care will take care of this (e.g.
> not just applying some absurdly high force constant and fast pulling, in
> which case you'd just be obliterating the membrane).
>
> -Justin
>
> >
> > On Sat, 12 May 2018 at 8:06 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> It's clear that pulling on a membrane protein will affect the behavior
> of
> >> the lipids in the membrane.
> >>
> >> Mark
> >>
> >> On Sat, May 12, 2018, 14:21 RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
> >>
> >>> Dear users,
> >>>
> >>> I have a complex [ dimer ] membrane protein. I want to perform sMD for
> >> this
> >>> complex structure. Is it valid and possible  to perform pull code for
> the
> >>> complex protein structure in the presence of lipid bilayer ?
> >>>
> >>> If yes, will it not disturb the lipid configurations of the system?
> >>>
> >>> Thank you.
> >>> --
> >>> *Regards,*
> >>> *Rahul *
> >>> --
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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-- 
*Regards,*
*Rahul *