[gmx-users] Vacuum disappear after NPT equilibration?

[Mark Abraham]

Justin's suggestion sounds reasonable. Your approach would have to have
enough water that there is no perturbation upon the water interacting with
the bilayer from the water-vacuum interface. That seems prohibitive to
compute and/or demonstrate...

Mark


On Sat, Jan 18, 2014 at 9:05 PM, Guangwei Jiang
<guangwei.jiang at qmul.ac.uk>wrote:

> Hi, Mark,
>
> I hope to introduce the ions into two water compartments above and below
> the lipid bilayers. But with the vacuum, I can block the ions flowing into
> the other side. This may overcome the case from periodic boundary condition.
>
> But I need to have such a stable structure with vacuum. Do you have any
> suggestions towards the equilibration?
>
> Thanks very much!
>
> Regards,
> Guangwei
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
> Abraham <mark.j.abraham at gmail.com>
> Sent: Saturday, January 18, 2014 5:21 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Vacuum disappear after NPT equilibration?
>
> Hi,
>
> Why are you trying to maintain a region of vacuum while changing the
> density of the rest?
>
> Mark
>
>
> On Sat, Jan 18, 2014 at 3:02 PM, Guangwei Jiang
> <guangwei.jiang at qmul.ac.uk>wrote:
>
> > Thanks, Justin!
> >
> > But I am still puzzled about the way to do equilibration without NPT.
> >
> > How can we realize the equilibration for a reasonable density in such
> > vacuum scheme?
> >
> > Forgive me the stupid question. Thanks very much!
> >
> > Regards,
> > Guangwei
> >
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin
> > Lemkul <jalemkul at vt.edu>
> > Sent: Friday, January 17, 2014 8:59 PM
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] Vacuum disappear after NPT equilibration?
> >
> > On 1/17/14, 2:13 PM, Guangwei Jiang wrote:
> > > Thanks very much, Justin!
> > >
> > > Yes, in NVT equilibration, the box size does not change. But can I skip
> > the NPT equilibration process to the MD modulation directly?
> > >
> >
> > You should equilibrate the system and then collect data under the
> ensemble
> > that
> > you need to model.  There is no one, single, universal way to equilibrate
> > a system.
> >
> > > Besides, in NPT equilibration, the semiisotropic pressure coupling is
> > used. Does that mean the box in z-axis is already incompressible? But we
> > can see the box in z-axis is still shrinking.
> > >
> >
> > No, that means the scaling of box vectors in x and y are uniform and z is
> > independent.  You can, in theory, make the z direction fixed by setting
> the
> > compressibility along z to zero.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >
> > ==================================================
> > --
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