[gmx-users] syntax for index file in "gmx distance"

[laura O.]

Hi

http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#command-changes-between-versions

Em dom, 17 de fev de 2019 09:22, ZHANG Cheng <272699575 at qq.com escreveu:

> I think I know now:
>
>
> gmx distance -f dynamic_noPBC.xtc -s dynamic -n index.ndx -select 'group 0
> plus group 1' -oall
>
>
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng"<272699575 at qq.com>;
> Date:  Sun, Feb 17, 2019 08:06 PM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> Subject:  syntax for index file in "gmx distance"
>
>
>
> My gro file looks like this
>
>
> $ Martini system from C226S.pdb
> $ 72758
> $     1ASP     BB    1  15.982   3.547   3.592
> $     1ASP    SC1    2  15.989   3.335   3.842
> $     2ILE     BB    3  15.668   3.625   3.593
> $     2ILE    SC1    4  15.538   3.345   3.620
> $     3GLN     BB    5  15.590   3.886   3.462
> $     3GLN    SC1    6  15.908   4.021   3.297
>
>
>
>
>
> I tried:
> $ gmx distance -f dynamic_noPBC.xtc -s dynamic -n index.ndx -oall
>
>
> in which the index.ndx is
> $ [ atom ]
> $ 1
> $ [ atom ]
> $ 19
>
>
>
> But I was told:
> $ Available static index groups:
> $  Group  0 "atom" (1 atoms)
> $  Group  1 "atom" (1 atoms)
> $ Specify any number of selections for option 'select'
> $ (Position pairs to calculate distances for):
> $ (one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
>
>
>
> How should I proceed with this?
>
>
> Is there a simple example example for the index.ndx? I could not find good
> answers at
> http://manual.gromacs.org/archive/5.0.3/online/ndx.html
> http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-distance.html
>
>
> Thank you.
>
>
> Cheng
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