[gmx-users] Using h-angles taking to much time
harpreetsingh05 at hotmail.com
Sat Oct 20 08:32:56 CEST 2007
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
-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...
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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