Can someone please provide some guidance, I am new at AMBER and running MD simulations on a ssDNA 10mer. I have read everything I can find to determine why my mdout file does not provide values for EHBOND and RESTRAINT. I assume it involves the parameters I set up, but after changing several, turning off SHAKE and extensive reading, nothing I do is providing a value for either of these forces.
Thanks for your help!
Ron
NSTEP = 500000 TIME(PS) = 21020.000 TEMP(K) = 298.82 PRESS = 161.0
Etot = -28161.5253 EKtot = 6071.2019 EPtot = -34232.7271
BOND = 80.5684 ANGLE = 162.6408 DIHED = 195.2299
1-4 NB = 84.6959 1-4 EEL = -1117.0626 VDWAALS = 4529.4582
EELEC = -38168.2577 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 2880.8285 VIRIAL = 2527.2284 VOLUME = 101728.1279
Density = 1.0126
Ewald error estimate: 0.1178E-03
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Received on Thu Nov 08 2012 - 15:00:02 PST
