Re: [gmx-users] Center of mass motion removal for partial filled PBC box

2011-01-27 Thread Mark Abraham
On 28/01/2011 4:25 AM, WU Yanbin wrote: Dear GMXers, I would like to reproduce the water droplet contact angle on graphite surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.; Koumoutsakos, P. /J. Phys. Chem. B/ *2003*, /107/, 1345-1352. The box size is 20nm by 20nm by 30nm. Graphite i

[gmx-users] Center of mass motion removal for partial filled PBC box

2011-01-27 Thread WU Yanbin
Dear GMXers, I would like to reproduce the water droplet contact angle on graphite surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.; Koumoutsakos, P. *J. Phys. Chem. B* *2003*, *107*, 1345-1352. The box size is 20nm by 20nm by 30nm. Graphite is represented by a two-layer carbon sheet. Af

Re: [gmx-users] center of mass motion

2007-01-16 Thread David van der Spoel
Cherry Y. Yates wrote: Dear Gromacs users and developers, I am studying a system consisting of six molecules (3 groups). I would like to keep the center-of-mass motion of each molecule with the system having zero center-of-mass motion. So I set comm_mode=Linear. In the simulation, immediately th

[gmx-users] center of mass motion

2007-01-16 Thread Cherry Y. Yates
Dear Gromacs users and developers, I am studying a system consisting of six molecules (3 groups). I would like to keep the center-of-mass motion of each molecule with the system having zero center-of-mass motion. So I set comm_mode=Linear. In the simulation, immediately the center-of-mass motion o

Re: [gmx-users] center of mass motion in lipid bilayer

2007-01-11 Thread David van der Spoel
Jian Dai wrote: Hello, everyone: I have a system which is composed of a lipid bilayer and water layers upon each monolayers. Now the problem is that after the simulation, the lipid bilayer shift upward inside the simulation box , and makes the upper water layer thinner, while the lower water

[gmx-users] center of mass motion in lipid bilayer

2007-01-11 Thread Jian Dai
Hello, everyone: I have a system which is composed of a lipid bilayer and water layers upon each monolayers. Now the problem is that after the simulation, the lipid bilayer shift upward inside the simulation box , and makes the upper water layer thinner, while the lower water layer thicker. In md