[gmx-users] wall problem

[Justin Lemkul]

On 2/4/14, 10:59 AM, Albert wrote:
> Hello Justin:
>
> I took your advices and submit the system to MD simulations. After NVT, the
> vacuum layer was still there. However, my pbc box shrinked to its orginal size
> after NPT, and the vacuum layer was disapeared.... here is my compreasiblity
> settings:
>
>
> ; Pressure coupling parameters
> pcoupl        = berendsen        ; Pressure coupler used under NPT conditions
> pcoupltype    = semiisotropic            ; Isotropic scaling in the x-y
> direction, independent of the z direction
> tau_p        = 1.0    1.0            ; Coupling time constant (ps)
> ref_p        = 1.0    1.0            ; Reference pressure for coupling, x-y, z
> directions (bar)
> compressibility = 4.5e-5    4.5e-5        ; Isothermal compressibility (bar^-1)
>
>
> I enlarged the vacuum layer in each leaflet around 3nm.
>

This is exactly the same issue that was discussed last week.  Please read those 
posts.

-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
http://mackerell.umaryland.edu/~jalemkul

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