[gmx-users] gromacs 5.0 tools: gmx distance and gmx mindist time series

[Ullmann, Thomas]

For the record, the problem of not getting the output expected from gmx distance
may have been related to a bug fixed here: https://gerrit.gromacs.org/#/c/4843/1

Happy computing,
Thomas.

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R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullmann at mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
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________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abraham at gmail.com]
Sent: Thursday, May 07, 2015 4:52 PM
To: oliwias; gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] gromacs 5.0 tools: gmx distance and gmx mindist        time series

Hi,

On Thu, May 7, 2015 at 3:59 PM oliwias <oliwias at ethz.ch> wrote:

> 1. How can I get rid of the inconsistency? Did I use the wrong options
> for gmx_trjcat?
>

Depends whether you care. You wrote files with two different output
periods, and now you want to treat them as a continuous thing, which in one
sense they are not. Whether that matters depends what you want to do next,
and that's your call. trjconv has functionality that would e.g. let you
extract only the frames from one set of trajectories that will match the
period of the other, and then you can trjcat the lot together.

You can also first get gmx distance working on your partial trajectories,
to solve that part of the problem independently.

2. About the distances - for gromacs 4.6.7 I used:
> printf "A\nB\n" | g_dist -s md_2.tpr -f md.xtc -n sys.ndx -o dist.xvg
> -dt 100
>
> for gromacs 5.0 I used:
> printf "A\nB\n" | gmx distance -s md_2.tpr -f md.xtc -n sys.ndx -oall
> dist_all.xvg -oav dist_av.xvg -oh dist_h.xvg -dt 100 -tu ns
>

You're doing two different things here. You've set the units with -tu to
ns, and so (IIRC) -dt is interpreted in that context. I don't know if
that's part of the problem.

More important is that you read gmx distance -h, compare with g_dist -h and
realise that the functionality in gmx distance is much greater than g_dist.
You need to use the selection syntax to get the COM for your two index
grounds, which g_dist did for you because that's all it could do.

Mark

Doees that indicate anything?
>
> Cheers,
> oliwia
>
> On 07.05.2015 15:43, Mark Abraham wrote:
> > Hi
> >
> > On Thu, May 7, 2015 at 3:34 PM oliwias <oliwias at ethz.ch> wrote:
> >
> >> Hi Mark,
> >>
> >> 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.
> >>
> >
> > Yes, that's what the message is telling you, in case you didn't know,
> > messed up, etc.
> >
> >
> >> 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?
> >>
> >
> > Neither can we, since you didn't tell us what you did when you tried to
> > get
> > the time series. Here you talked about how you built your inputs.
> >
> > Mark
> >
> >
> >> Cheers,
> >> oliwia
> >>
> >>
> >> On 07.05.2015 14:59, Mark Abraham wrote:
> >> > Hi,
> >> >
> >> > Time series are what gmx distance does... see gmx distance -h, of
> >> > course.
> >> > If it's not working for you, you'll have to tell us exactly what you
> >> > tried,
> >> > what output you got, what's not suitable, etc., and check that your
> >> > input
> >> > files contain what you think they do (e.g. with gmx check)
> >> >
> >> > Mark
> >> >
> >> > 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
> >> >> hand,
> >> >> 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!
> >> >> oliwia
> >> >> --
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