Re: [gmx-users] interface

2012-02-22 Thread Mark Abraham
To:* Discussion list for GROMACS users *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 ens

RE: [gmx-users] interface

2012-02-21 Thread Dallas Warren
What does it look like when you visualise the coordinate file? That is how you can answer that question, as we certainly can't. And as you will soon find out, you cannot have a single interface in a simulation box, you have to have two. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug

Re: [gmx-users] interface

2012-02-21 Thread Mark Abraham
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