[gmx-users] Using h-angles taking to much time

harpreet singh harpreetsingh05 at hotmail.com
Sat Oct 20 08:32:56 CEST 2007

Dear Sir,

I am running Molecular dynamics simulation. Using other constraints the program is running very fast but if  I am using constraints = h-angles or all-angles the program is taking too much of time (running since last 12 hours).

Kindly suggest me that is it the normal behavior of the program or something went wrong with my data.


  -nice    int      0  Set the nicelevel
      -[no]v   bool    yes  Be loud and noisy
       -time   real     -1  Take frame at or first after this time.
         -np    int      1  Generate statusfile for # nodes
-[no]shuffle   bool     no  Shuffle molecules over nodes
   -[no]sort   bool     no  Sort molecules according to X coordinate
-[no]rmvsbds   bool    yes  Remove constant bonded interactions with vi
       -load string         Releative load capacity of each node on a
                            parallel machine. Be sure to use quotes aro
                            the string, which should contain a number f
                            each node
    -maxwarn    int     10  Number of warnings after which input proces
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waa
  -[no]renum   bool    yes  Renumber atomtypes and minimize number of

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
turning all bonds and H angles into constraints...

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