Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Albert
On 02/12/2013 03:33 PM, Justin Lemkul wrote: gmxcheck is your friend, as well as the wiki. http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File A checkpoint file is always written at the last step of the simulation, which seems to be what you were asking for previously. -Just

Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Justin Lemkul
On 2/12/13 9:32 AM, Albert wrote: On 02/12/2013 03:28 PM, Justin Lemkul wrote: Extract it from the .cpt file that corresponds to that frame. -Justin thanks a lot for such helpful comments. I found that the md production produced two .cpt file: state.cpt state_prev.cpt I am not sure whic

Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Albert
On 02/12/2013 03:28 PM, Justin Lemkul wrote: Extract it from the .cpt file that corresponds to that frame. -Justin thanks a lot for such helpful comments. I found that the md production produced two .cpt file: state.cpt state_prev.cpt I am not sure which one would be the one I need D

Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Justin Lemkul
On 2/12/13 9:25 AM, Albert wrote: On 02/12/2013 03:19 PM, Justin Lemkul wrote: Velocities are not stored in .xtc files. They are stored in .trr files, if nstvout != 0 in the .mdp file. -Justin Hi Justin: thanks for kind comments. I used the following settings and I didn't generate .trr

Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Albert
On 02/12/2013 03:19 PM, Justin Lemkul wrote: Velocities are not stored in .xtc files. They are stored in .trr files, if nstvout != 0 in the .mdp file. -Justin Hi Justin: thanks for kind comments. I used the following settings and I didn't generate .trr file: nstxout= 0

Re: [gmx-users] velocity was not present from trjconv

2013-02-12 Thread Justin Lemkul
On 2/12/13 9:17 AM, Albert wrote: Hello: I am using Gromacs4.6 and I extract one of my frame into .gro file by command: trjconv_mpi -f md.xtc -s md.tpr -dump 25000 -o md.gro I found that the velocity information was not present in this 25ns-md.gro file: Velocities are not stored in .xtc

[gmx-users] velocity was not present from trjconv

2013-02-12 Thread Albert
Hello: I am using Gromacs4.6 and I extract one of my frame into .gro file by command: trjconv_mpi -f md.xtc -s md.tpr -dump 25000 -o md.gro I found that the velocity information was not present in this 25ns-md.gro file: Generated by trjconv : Protein t= 25000.0 54178 1TYR N