[gmx-users] interface

Mark Abraham 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
> Sara
> ------------------------------------------------------------------------
> *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 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
> -- 
> gmx-users mailing list gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120223/38b24449/attachment.html>

More information about the gromacs.org_gmx-users mailing list