Hello and my apologies in advance for a novice question.
I have run peptides in implicit solvent with relative success in the past but ran into trouble when I tried explicit solvent. I backed up a step and found that I got into trouble just following the DNA tutorial (B1) with the coordinates looking like a child's scribble (picture below) as soon as I begin the heating MD (the minimization output looks normal.) I only get these results for the explicit solvent; vacuum and gb cases look normal. Also, the energies from the explicit heat.out file look reasonable to me (at least, nothing seems to explode)which is unexpected given the VMD picture below.
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NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -43070.3250 EKtot = 0.0000 EPtot = -43070.3250 BOND = 18.6297 ANGLE = 96.2624 DIHED = 394.1982 1-4 NB = 147.4288 1-4 EEL = -347.4700 VDWAALS = 7031.4029 EELEC = -50410.7769 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------
NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 59.58 PRESS = 0.0 Etot = -35478.5274 EKtot = 1115.3875 EPtot = -36593.9148 BOND = 41.9949 ANGLE = 130.9893 DIHED = 403.8286 1-4 NB = 153.2056 1-4 EEL = -349.9076 VDWAALS = 5183.7767 EELEC = -42178.1906 EHBOND = 0.0000 RESTRAINT = 20.3883 EAMBER (non-restraint) = -36614.3031 ------------------------------------------------------------------------------
NSTEP = 200 TIME(PS) = 0.400 TEMP(K) = 103.92 PRESS = 0.0 Etot = -33866.6135 EKtot = 1945.3761 EPtot = -35811.9896 BOND = 62.8891 ANGLE = 161.3373 DIHED = 411.2359 1-4 NB = 149.8413 1-4 EEL = -342.2597 VDWAALS = 5211.2030 EELEC = -41501.9409 EHBOND = 0.0000 RESTRAINT = 35.7043 EAMBER (non-restraint) = -35847.6939 ------------------------------------------------------------------------------
Any suggestions would be appreciated. Again, I'm sorry for the novicequestion. Of course, I would be happy to provide further information if it would be useful.
Regards,
Heather
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Received on Thu Jan 17 2013 - 11:00:03 PST
