mra_bu at yahoo.com
Thu Feb 23 07:27:49 CET 2012
Thank you very much from your reply.
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, February 23, 2012 5:24 AM
Subject: Re: [gmx-users] interface
On 22/02/2012 10:34 PM, mohammad agha wrote:
>Thank you very much from your reply.
>I see a box that the half of it consists of water and another half of box is void, but when I run md.mdp for production simulation all of water molecules dispersed in total of box and I don't see interface and total of box filled by water.
What did you expect a liquid in contact with a vacuum to do?
>Can you help me to construct the air/water interface, Please?
First you need to decide how you're going to produce a valid model
of *air* which is different from a *vacuum*. Then you need to find
parameters for such a model. Then it's the same kind of approach as
a mixed-solvent system (see gromacs webpage), only here it will be
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Sent: Wednesday, February 22, 2012 12:59 AM
>Subject: Re: [gmx-users] interface
>On 22/02/2012 3:11 AM, mohammad agha wrote:
>Dear Gromacs Specialists,
>>I made a box consists of water with box lengths: 6nm * 6nm * 6nm , then I equilibrated it with NPT ensemble, box size increased to 6.66176, then I kept the x- and y-dimensions fixed, and double the system size in z as following:
>>editconf -f pr1.gro -o newbox1.gro -box 6.66176 6.66176 13.32352 -center 3.33088 3.33088 3.33088
>>Next that, I placed one surfactant in center
of water phase as following:
>>editconf -f surfactant.gro -o newbox-cta.gro -box 6.66176 6.66176 13.32352 -center 3.33088 3.33088 1.66544
>>genbox -cp newbox-cta.gro -cs newbox1.gro -o
>>and I added one ion to my system, then ran md.mdp for production simulation.
>>Do I have one air/water interface in my system?
>You need to use visualization software and see if the
configuration looks like you intend it to look. You
certainly don't have an air-water interface if one of
them is vacuum.
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