Mark.Abraham at anu.edu.au
Thu Feb 23 02:54:23 CET 2012
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
> Best Regards
> *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
>> /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
>> /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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