[gmx-users] Vacuum disappear after NPT equilibration?

[Guangwei Jiang]

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
>
> ==================================================
> --
> 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.
>
--
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.