[gmx-users] problem in making a trajectory
francesca.vitalini11 at gmail.com
Sat Jun 16 13:41:33 CEST 2012
this is my trjcat command
I'm using the settime command to have each structure at a different time
step. If I was using it wrongly please correct me.
Thanks in advance for all the help.
2012/6/16 Justin A. Lemkul <jalemkul at vt.edu>
> On 6/16/12 6:48 AM, francesca vitalini wrote:
>> Dear Gromacs Users,
>> While making a trajectory connecting different gro files I got the
>> output which I don't understand.
>> Continue writing frames from
>> t=1 ps, frame=0
>> Last frame 0 time 0.000
>> WARNING: Frames around t=1.000000 ps have a different spacing than the
>> might be a gap or overlap that couldn't be corrected automatically.
>> Reading frames from gro file 'Protein', 15230 atoms.
>> Reading frame 0 time 0.000
>> WARNING: Couldn't find a time in the frame.
>> Can anyone explain to me the implication of this warning message?
> Trajectories need time information, .gro files don't have any. In the
> absence of your trjcat command, I can only assume you're not using -settime
> to specify what time point to which each frame corresponds. If that's not
> the case, please provide the command you are using.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin
vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de
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