On 10/10/16 3:52 PM, Alex wrote:
Thanks.

I used the "direction-periodic",  along with "semiisotropic" with zero
compressibility in Z direction to have also NPT equilibration in each
windows. Below is the final pressure after NPT equilibration with 1 bar
reference, I hope it would be ok?!

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                   -252.127       0.66    165.053    3.15753  (bar)


Even considering the magnitude of the error bar, that's not achieving 1 bar.

-Justin

Regards,
Alex


On Mon, Oct 10, 2016 at 8:25 PM, Justin Lemkul <jalem...@vt.edu> wrote:



On 10/10/16 4:57 AM, Alex wrote:

Thanks for your response.

My question is not in the sampling step as I have already pulled away two
parts and even picked out the configuration of each windows. But my
question is about simulation in each individual windows toward WHAM.

You means in the step six of the tutorial no necessarily need to do any
NVT
or NPT before production simulation?


It's no different from any simulation.  You need to equilibrate under the
ensemble you're going to use for data collection before you actually do
that data collection.  If you would normally want NPT for a Gibbs free
energy and can't get it for whatever reason (like the algorithmic
limitation mentioned), then equilibrate with NPT to arrive at the desired
density, and continue with NVT.  You won't get a Gibbs free energy, you'll
get the Helmholtz free energy, but at least the density will be right.
Otherwise, build a bigger system that removes the restrictions of
direction_periodic and use NPT.

-Justin


Thanks,
Alex


On Mon, Oct 10, 2016 at 2:17 AM, Justin Lemkul <jalem...@vt.edu> wrote:



On 10/8/16 2:46 PM, Alex wrote:

Dear gromacs user,

In a PMF simulation of a short peptide on solid surface, I am using the
"direction-periodic" as "pull-coord1-geometry" in the Z  direction, then
as
you know the equilibration of the system in NPT ensemble is not doable
for
the individual windows. So, for each windows of umbrella sampling, I am
going to do minimization and NVT equilibration and then MD production. I
was wondering if the lack of the NPT  equilibration would not badly
affect
on the result PMF? If so, how can I compensate it somehow?


All you're doing is sampling under a different ensemble.  There's no
reason to think that a PMF requires an NPT ensemble.

-Justin

By the way, I nicely minimized. equilibrated (both NVT and NPT) and a 60
ns

of production simulation of my initial system before coming to the
pulling
step.

Thanks.

Regards,
Alex


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

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.
Baltimore, MD 21201

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

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.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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

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.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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