[gmx-users] Re: Help again!!!!!!!
lindahl at stanford.edu
Mon Oct 7 22:50:46 CEST 2002
Try to send the mails to the mailing list; that way more people will
read your mail,
and the answers will be archived.
> I am afraid I did understand your answer. The output.gro file from the
>first minimization is the file after_em.gro. When I use grompp in it with
>the option -t, GROMACS gives the message: "fatal error: grompp.mdp doesn't
The grompp commands needs a file with the options. You specify it with
the -f option
and the default value is grompp.mdp. Work through the getting started
it doesn't make sense!
>I tryed also, to create the file after_em.top from after_em.gro but, when I
>try to run it, GROMACS gives me the message: "Fatal error: number of
>coordinates in coordiante file (after_em.gro, 143593) does not match
>topology file (after_em.top, 143590)". How can it be possible if the
>after_em.top file was created from the after_em.gro file ? And how can I
>solve this ?
The .top file is the topology of your system (i.e. it specifices the
types of atoms and
all parameters) and should be exactly the same for all your runs - you
try to create a new topology after the energy minimization.
You might have overwritten your topology with a coordinate file or
>Another question I have is the following one:
> In several minimizations I have run, GROMACS is writing in the top of the
>em.job file the following warning: "1 - 4 interaction at distance larger
>than 1 +09 Fmax = 4,99952e +11. These are ignored for the rest of the
>simulation. turn on -debug for more information." How can I know which
>interaction is at that distance and how can I turn on -debug for more
>Sorry for so many doubts. That's because I am a beginer yet.
Just add the flag '-debug' when running the command in question (e.g.
will add A LOT more information in the .log files.
More information about the gromacs.org_gmx-users