[gmx-users] Calculation of Temperature of Cluster

2013-04-08 Thread Rasoul Nasiri
Dear All, I tried to use g_clustsize_d program for estimation of temperature of cluster/nanodroplet but the temperature output file is empty. Could you comment where is the problem? Please note that I can get Temperature of system using g_energy_d but I'm interest to know cooling effect of

Re: [gmx-users] Calculation of Temperature of Cluster

2013-04-08 Thread Justin Lemkul
On Mon, Apr 8, 2013 at 9:01 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Dear All, I tried to use g_clustsize_d program for estimation of temperature of cluster/nanodroplet but the temperature output file is empty. Could you comment where is the problem? Not without seeing your command

Re: [gmx-users] Calculation of Temperature of Cluster

2013-04-08 Thread Rasoul Nasiri
Bellow is my command which I used: g_clustsize_d -f traj.xtc -s topol.tpr -n n.ndx -nc nclust.xvg -mc maxclust .xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg Rasoul On Mon, Apr 8, 2013 at 2:04 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 8, 2013 at 9:01 AM, Rasoul

Re: [gmx-users] Calculation of Temperature of Cluster

2013-04-08 Thread Justin Lemkul
On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Bellow is my command which I used: g_clustsize_d -f traj.xtc -s topol.tpr -n n.ndx -nc nclust.xvg -mc maxclust .xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg Then it is exactly what I said.

Re: [gmx-users] Calculation of Temperature of Cluster

2013-04-08 Thread Rasoul Nasiri
Justin, Thanks for your comment. Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still encountering to empty file for temperature. Rasoul On Mon, Apr 8, 2013 at 2:10 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri nasiri1...@gmail.com

Re: [gmx-users] Calculation of Temperature of Cluster

2013-04-08 Thread Justin Lemkul
On Mon, Apr 8, 2013 at 9:24 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Justin, Thanks for your comment. Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still encountering to empty file for temperature. Can you please provide the gmxcheck output for the .trr file? I

Re: [gmx-users] Calculation of Temperature of Cluster

2013-04-08 Thread Rasoul Nasiri
One suggestion, Is there any chance to retrieve trajectory of un-evaporated molecules using one of gromacs tools? Now I have a ndx file which show number of atoms stayed in drop, Which one is better? I mean if I can get trajectory (position+velocity) unevaporated molecules, I would be able

Re: [gmx-users] Calculation of Temperature of Cluster

2013-04-08 Thread Justin Lemkul
On Mon, Apr 8, 2013 at 9:39 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: One suggestion, Is there any chance to retrieve trajectory of un-evaporated molecules using one of gromacs tools? Now I have a ndx file which show number of atoms stayed in drop, Sure, that's what trjconv does.