[gmx-users] gromacs 5.0 tools: gmx distance and gmx mindist time series
oliwias at ethz.ch
Thu May 7 15:33:28 CEST 2015
I'm quite new to gromacs, so thanks for your help! I have an md
trajectory in 3 files. I used:
gmx_trjcat -f md1.xtc md2.xtc md3.xtc -o md.xtc -settime
in order to get one file for analysis. I set the time of the first file
to 0.0, and for the next two files I set the time to "c" (continue, I
suppose). When I run:
gmx check -f md.xtc -s1 md_2.tpr -c
I get a message:
"Timesteps at t=20000 don't match (2, 5)"
I don't know why... The only reason that comes to my mind is that
between run 1 and run 2 I changed the frequency of output.
Still, I don't understand why I get the time series when using the tool
from gromacs 4.6 (seems that it doesn't care about the timestep
mismatch), but not using gromacs 5.0?
On 07.05.2015 14:59, Mark Abraham wrote:
> Time series are what gmx distance does... see gmx distance -h, of
> If it's not working for you, you'll have to tell us exactly what you
> what output you got, what's not suitable, etc., and check that your
> files contain what you think they do (e.g. with gmx check)
> On Thu, May 7, 2015 at 2:38 PM oliwias <oliwias at ethz.ch> wrote:
>> Dear All,
>> I am trying to use the new gromacs 5.0 tools for analysis. I tried
>> multiple options but I can't get gmx distance and gmx mindist to print
>> out time series of distances. I only get the average. On the other
>> I had no problem with getting the time series with gromacs 4.6 g_dist
>> and g_mindist. Don't know if it's a problem of the code or if I just
>> don't know how to use the tool...
>> I'd appreciate your tips!
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