Re: [gmx-users] extracting coordinates from traj.xtc

2015-12-06 Thread Justin Lemkul
On 12/6/15 2:49 AM, mah maz wrote: Thank you. I tested gmxdump and also trjconv -dump and compared traj.trr and traj.xtc. You are right both have the same data. I just need the coordinates to be readable a printable in a file now. Although I can write a program to extract the coordinates from g

Re: [gmx-users] extracting coordinates from traj.xtc

2015-12-06 Thread Justin Lemkul
On 12/6/15 2:56 AM, mah maz wrote: And also, if I want velocities for every step what can I do? nstvout = 1 -Justin Thanks! On Sun, Dec 6, 2015 at 11:19 AM, mah maz wrote: Thank you. I tested gmxdump and also trjconv -dump and compared traj.trr and traj.xtc. You are right both have the

Re: [gmx-users] extracting coordinates from traj.xtc

2015-12-05 Thread mah maz
And also, if I want velocities for every step what can I do? Thanks! On Sun, Dec 6, 2015 at 11:19 AM, mah maz wrote: > Thank you. I tested gmxdump and also trjconv -dump and compared traj.trr > and traj.xtc. You are right both have the same data. I just need the > coordinates to be readable a pr

Re: [gmx-users] extracting coordinates from traj.xtc

2015-12-05 Thread mah maz
Thank you. I tested gmxdump and also trjconv -dump and compared traj.trr and traj.xtc. You are right both have the same data. I just need the coordinates to be readable a printable in a file now. Although I can write a program to extract the coordinates from gmxdump the way I need, it seems a bit t

Re: [gmx-users] extracting coordinates from traj.xtc

2015-12-04 Thread Justin Lemkul
On 12/3/15 11:57 AM, mah maz wrote: Thanks Justin! I checked the run and it seemed ok. The fact is, the data I get by g_traj -f traj.trr -ox is reasonable (although I didnt set nstxout it was set every 100 step by default), while the same command with g_traj -f traj.xtc -ox gives wrong coordina

Re: [gmx-users] extracting coordinates from traj.xtc

2015-12-03 Thread mah maz
Thanks Justin! I checked the run and it seemed ok. The fact is, the data I get by g_traj -f traj.trr -ox is reasonable (although I didnt set nstxout it was set every 100 step by default), while the same command with g_traj -f traj.xtc -ox gives wrong coordinates. Since I need coordinates for every

Re: [gmx-users] extracting coordinates from traj.xtc

2015-12-02 Thread Justin Lemkul
On 12/1/15 8:21 AM, mah maz wrote: Thank you Justin. I expected that only water molecules are written in .xtc but all the others are there! g_traj -f traj.xtc -ox gives numbers like 1.64e-318 for all frames! How can I get real coordinates from .xtc? If you've got unexpected content, you need

Re: [gmx-users] extracting coordinates from traj.xtc

2015-12-01 Thread mah maz
Thank you Justin. I expected that only water molecules are written in .xtc but all the others are there! g_traj -f traj.xtc -ox gives numbers like 1.64e-318 for all frames! How can I get real coordinates from .xtc? Thanks! On Tue, Dec 1, 2015 at 10:34 AM, mah maz wrote: > Dear all, > I have some

Re: [gmx-users] extracting coordinates from traj.xtc

2015-12-01 Thread Justin Lemkul
On 12/1/15 2:04 AM, mah maz wrote: Dear all, I have some problems extracting data from traj.xtc. The command " g_traj -s -ox" doesn't give reasonable coordinates. I tried "trjconv" but again Why aren't they reasonable? That also couldn't have been your command, which requires at least a fil

[gmx-users] extracting coordinates from traj.xtc

2015-11-30 Thread mah maz
Dear all, I have some problems extracting data from traj.xtc. The command " g_traj -s -ox" doesn't give reasonable coordinates. I tried "trjconv" but again couldn't get any results. Note that I have nstxtcout = 1 and xtc_grps = water in my .mdp file. Any help is appreciated. Thank you! -- Gromacs