Re: [gmx-users] Occupancy for a distance cut off

2013-02-11 Thread ram bio
Thank you!! On Mon, Feb 11, 2013 at 8:29 PM, Justin Lemkul wrote: > > > On 2/11/13 9:16 PM, ram bio wrote: >> >> Hi Justin, >> >> Thanks for the suggestion. >> >> I executed the following command: >> >> g_dist -f n101c2naclprod2-12nsvrpr.trr -s >> n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist

Re: [gmx-users] Occupancy for a distance cut off

2013-02-11 Thread Justin Lemkul
On 2/11/13 9:16 PM, ram bio wrote: Hi Justin, Thanks for the suggestion. I executed the following command: g_dist -f n101c2naclprod2-12nsvrpr.trr -s n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o N101Cbest2NACL606S336HG1.xvg and the output was distance calculated for every 10 fr

Re: [gmx-users] Occupancy for a distance cut off

2013-02-11 Thread ram bio
Hi Justin, Thanks for the suggestion. I executed the following command: g_dist -f n101c2naclprod2-12nsvrpr.trr -s n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o N101Cbest2NACL606S336HG1.xvg and the output was distance calculated for every 10 frames in nm as under: t: 11870 336 SER

Re: [gmx-users] Occupancy for a distance cut off

2013-02-11 Thread Justin Lemkul
On 2/11/13 6:15 PM, ram bio wrote: Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output is in the form of xvg file, but I am looking for t

[gmx-users] Occupancy for a distance cut off

2013-02-11 Thread ram bio
Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output is in the form of xvg file, but I am looking for the occupancy for a cut off distance (3.