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

[oliwias]

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

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

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
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >> * For (un)subscribe requests visit
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >> send a mail to gmx-users-request at gromacs.org.
>> >>
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> 
> --
> Gromacs Users mailing list
> 
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.