On 22/02/2012 10:34 PM, mohammad agha wrote:
Dear Mark,
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 mixed
fluid.
Mark
Best Regards
Sara
------------------------------------------------------------------------
*From:* Mark Abraham <mark.abra...@anu.edu.au>
*To:* Discussion list for GROMACS users <gmx-users@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 newbox2.gro/
/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.
Mark
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