[gmx-users] Re: Help again!!!!!!!

[Erik Lindahl]

Hi,

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 
>exist". 
>
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 
excercise if
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 
definitely shouldn't
try  to create a new topology after the energy minimization.

You might have overwritten your topology with a coordinate file or 
something...

>
>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 
>information ? 
>Sorry for so many doubts. That's because I am a beginer yet. 
>  
>

Check http://www.gromacs.org/faq/

Just add the flag '-debug' when running the command in question (e.g. 
mdrun). This
will add A LOT more information in the .log files.

Cheers,

Erik

>  
>