[gmx-users] NVT, NPT and then pulling?

[Steven Neumann]

Thank you Justin

On Wed, Jun 27, 2012 at 9:36 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 6/27/12 4:30 PM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I am wondering whether would you advise to run NVT, NPT (position
>> restrained) and before the pulling simulation e.g of the ligand from
>> protein-ligand complex? As I saw in Justin tutorial he equilibrate the
>> system with only NPT ensemble before pulling. Is that really sufficent
>> e.g. for 200 ps?
>>
>
> There is no catch-all equilibration scheme that works universally.  NVT and
> NPT are commonly run in sequence.  My systems in the tutorial are quite
> robust and a single NPT phase is sufficient.  Please do not assume that this
> is universally true.  Your protocol should be based on how stable your
> systems are and how well your desired observables converge, but that much is
> true of every simulation.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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