[gmx-users] SMD regarding

[Justin Lemkul]

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 *
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================