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.
Regards
-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
sites
-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
stops
-[no]check14 bool no Remove 1-4 interactions without Van der Waa
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
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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