[gmx-users] problem in making a trajectory

francesca vitalini francesca.vitalini11 at gmail.com
Sat Jun 16 14:09:28 CEST 2012 

Yes I do have a trajectory and gmxcheck doesn't complain,
this is the output

Checking file ./300-65-100/300-65-100_traj_tot.xtc
Reading frame       0 time    1.000
# Atoms  15230
Precision 0.001 (nm)
Last frame          3 time    4.000


Item        #frames Timestep (ps)
Step             4    1
Time             4    1
Lambda           0
Coords           4    1
Velocities       0
Forces           0
Box              4    1

gcq#20: "Check Your Output" (P. Ahlstrom)


I was just wandering if the warning had any implication for the later use
of the trajectory.

Thank you very much for your help

Francesca



2012/6/16 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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 <jalemkul at vt.edu <mailto:jalemkul at 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://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
>>    ==============================**__==========
>>
>>
>>    --
>>    gmx-users mailing list gmx-users at gromacs.org <mailto:
>> gmx-users at gromacs.org>
>>    http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>>
>>    <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>
>>
>>    <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-request at gromacs.org
>>    <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >.
>>    Can't post? Read http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>>
>>    <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
>>
>> vitalini at zedat.fu-berlin.de <mailto:vitalini at zedat.fu-**berlin.de<vitalini at zedat.fu-berlin.de>
>> >
>> francesca.vitalini at fu-berlin.**de <francesca.vitalini at fu-berlin.de><mailto:
>> francesca.vitalini at fu-**berlin.de <francesca.vitalini at 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
>
> --
> gmx-users mailing list    gmx-users at 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-request at 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

vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de

+49 3083875776
+49 3083875412
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120616/1a927d3c/attachment.html>

More information about the gromacs.org_gmx-users mailing list