Re: [gmx-users] Distance calculation

2013-09-14 Thread Dr. Vitaly Chaban
g_mindist also has something useful in this direction, I guess. Dr. Vitaly V. Chaban On Sat, Sep 14, 2013 at 12:10 AM, Rama ramkishn...@gmail.com wrote: Hi , I there any tool to calculate distance between particular atom from one group(protein) to particular atom from another group(DMPC

[gmx-users] Distance calculation

2013-09-13 Thread Rama
Hi , I there any tool to calculate distance between particular atom from one group(protein) to particular atom from another group(DMPC lipid in Bilayer). For Example: protein backbone Amide(HN) to acyl chain carbon atom(C2D) in DMPC lipid. Thanks Rama -- View this message in context:

Re: [gmx-users] distance calculation

2012-09-20 Thread tarak karmakar
Thanks Mark. I was using the following command as I got it in the manual. g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg But I could not able to find the way how to specify the indices of the two desired atoms. ( suppose I want to plot the distance between atom no. 500 (protein

Re: [gmx-users] distance calculation

2012-09-20 Thread Mark Abraham
On 20/09/2012 4:21 PM, tarak karmakar wrote: Thanks Mark. I was using the following command as I got it in the manual. g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg But I could not able to find the way how to specify the indices of the two desired atoms. ( suppose I want to plot the

Re: [gmx-users] distance calculation

2012-09-20 Thread tarak karmakar
thanks a lot Mark On Thu, Sep 20, 2012 at 12:31 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 20/09/2012 4:21 PM, tarak karmakar wrote: Thanks Mark. I was using the following command as I got it in the manual. g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg But I could not

[gmx-users] distance calculation

2012-09-19 Thread tarak karmakar
Dear All, I want to calculate the distance between the nitrogen atom present in the ligand and the H- attached to the backbone of the protein along a long trajectory. So can anyone suggest me how to consider these two atoms to calculate and plot the distance along with the time ? -- Tarak --

Re: [gmx-users] distance calculation

2012-09-19 Thread tarak karmakar
Thanks Justin. But in my case I want to plot the distance between one atom in the backbone of the protein and other atom present in the ligand. Then how can I specify these two atoms I need for plotting the distance between them. On Thu, Sep 20, 2012 at 12:26 AM, Justin Lemkul jalem...@vt.edu

Re: [gmx-users] distance calculation

2012-09-19 Thread Mark Abraham
On 20/09/2012 2:05 PM, tarak karmakar wrote: Thanks Justin. But in my case I want to plot the distance between one atom in the backbone of the protein and other atom present in the ligand. Then how can I specify these two atoms I need for plotting the distance between them. g_dist treats the