VMD-L Mailing List

From: sarah k (dailycolors_at_gmail.com)
Date: Tue May 11 2010 - 02:29:02 CDT

dear all,

i ran a complex immersed in water box using gui. i first tried 5000
minimization and 5000000 MD steps. it resulted a fast simulation in 100
frames! then, i used 5000 minimization and 170000000 MD steps. again it was
simulated in 100 frames so faster than i expected.
I'm sure that there is a problem. I've tried some other complexes, protein+
ligands) the lasted much longer time and more frames.
i also tried other minimization step numbers. it just runs minimization. i
removed the water box and did the simulation again. this time MD was done
too but when i open *.dcd file into *.psf file VMD opens them but doesn't
display anything and when i want to plot RMSD it face error stating it can't
work with floating numbers. I've checked my *.log file. it was perfect.

it's very important in my research to run simulation in water box or sphere.
how can i fix all these problems?

Enjoy life,
Sarah K.