[gmx-users] Simulation in Constant pH simulation ...

[Catarina A. Carvalheda dos Santos]

Just to clarify.

What Justin is suggesting is not a constant-pH MD simulation (as the
protonation states won't be allowed to change during the simulation as
explained), but it might be a good starting point to understand if
different (fixed) protonation states will affect the properties of your
system (if you try different possibilities).
Constant-pH MD runs are more expensive than standard MD, so testing this
first might not be a bad idea.

Regards,


On 15 June 2016 at 16:52, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/15/16 11:49 AM, Nikhil Maroli wrote:
>
>> Hi,
>> Justin , thanks for your reply.
>> Actually, my system is cyclic peptide nanotube in water,which I made using
>> charmm-gui. Protonation option availbe  in " PDB reader " but how to
>> confirm the pH,based on protonation ? or is it possbile to make any
>>
>
> You don't "confirm the pH" because there is none.  You don't have
> titratable
> sites and you don't have H3O+ floating around.  The point of a fixed-charge
> simulation is to simulate the dominant protonation state that would be
> found at
> a given pH in a real, physical system.  The protonation states are chosen
> based
> on pKa values of those titratable moieties and which form will dominate at
> a
> given pH.
>
> changed after getting the out put
>>
>>
> I wouldn't try to make post-hoc changes.  Adding or deleting H atoms will
> change
> everything about the topology.  Set it up properly to start.
>
> -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.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK