[gmx-users] GFP Simulation

Dear Gmxers, I am working on a new project and I plan to do some molecular dynamic simulation on an engineered GFP molecule. I have been searching for the parameters for the GFP chromophore without success. Could some one help me? Any reference or parameters will be appreciated. Thanks, Juju

[gmx-users] -e -dt flags

Hi guys, I got a little shocked when I used the -e and -dt in g_hbond, why the default for - e is 0, on manual it says -e means last frame to read from trajectory. I know -b means First frame to read from trajectory with default 0, why do both default values are the same, and both from 0.

Re: [gmx-users] Check V for NVT‏

3:23:40 PM Subject: Re: [gmx-users] Check V for NVT‏ Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find Volume in the pool of the options. Can anyone

Re: [gmx-users] Check V for NVT‏

for NVT‏ On Fri, 13 Aug 2010 18:23:40 -0400 Justin A. Lemkul jalem...@vt.edu wrote: Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find Volume