On 6/16/12 7:54 AM, francesca vitalini wrote:
yes and I do.
By the way the version of GROMACS I'm using is the 3.3.1, I forgot to specify
that before.
OK, I see the same with version 4.5.5, but a trajectory is produced from my set
of .gro files and it is correct.
Continue writing frames from md_0_25.gro t=0 ps, frame=0
Last frame 0 time 0.000
WARNING: Frames around t=0.000000 ps have a different spacing than the rest,
might be a gap or overlap that couldn't be corrected automatically.
Reading frames from gro file 'Raft G96 system in water', 60523 atoms.
Reading frame 0 time 0.000
WARNING: Couldn't find a time in the frame.
lasttime 0
Continue writing frames from md_25_50.gro t=25 ps, frame=1
Last frame 0 time 0.000
WARNING: Frames around t=25.000000 ps have a different spacing than the rest,
might be a gap or overlap that couldn't be corrected automatically.
Reading frames from gro file 'Raft G96 system in water', 60523 atoms.
Reading frame 0 time 0.000
WARNING: Couldn't find a time in the frame.
lasttime 25
The key is to note that it is setting the times specified. Do you get an .xtc
file? What does gmxcheck tell you about it?
-Justin
2012/6/16 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
On 6/16/12 7:41 AM, francesca vitalini wrote:
Dear Justin,
this is my trjcat command
/home/cocktail/vitalini/__gromacs_special/bin/trjcat -f
/home/cocktail2/vitalini/__reverse_transformation_vacuum/__300-65-100/300-65-100___annealing.gro
/home/cocktail2/vitalini/__reverse_transformation_vacuum/__300-65-100/300-65-100___annealing2.gro
/home/cocktail2/vitalini/__reverse_transformation_vacuum/__300-65-100/300-65-100_min.gro
/home/cocktail2/vitalini/__reverse_transformation_vacuum/__300-65-100/300-65-100_min1.gro
-o
/home/cocktail2/vitalini/__reverse_transformation_vacuum/__300-65-100/300-65-100_traj___tot.xtc
-settime -cat
I'm using the settime command to have each structure at a different time
step.
If I was using it wrongly please correct me.
You should be prompted to then set a time value for each frame, is that not
the case?
-Justin
--
==============================__==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
--
gmx-users mailing list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
<http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
--
Francesca Vitalini
PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin
vital...@zedat.fu-berlin.de <mailto:vital...@zedat.fu-berlin.de>
francesca.vital...@fu-berlin.de <mailto:francesca.vital...@fu-berlin.de>
+49 3083875776
+49 3083875412
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
