Dear Amber Users,
I am trying to follow the protocols in
http://ambermd.org/tutorials/basic/tutorial3 to obtain some conformational
sampling for a small peptide of my interest. It turns out that during the
heating stages (~250K), the total energy of the system becomes +ve. I am heating
it upto 310K and I have pasted below the snapshots from the last heating run. I
am following the protocol in the tutorial.
NSTEP = 39950 TIME(PS) = 49.975 TEMP(K) = 310.94 PRESS = 0.0
Etot = 221.9592 EKtot = 457.8622 EPtot = -235.9030
BOND = 122.9774 ANGLE = 355.1161 DIHED = 464.4054
1-4 NB = 122.0431 1-4 EEL = 1446.9111 VDWAALS = -166.7690
EELEC = -2024.7384 EGB = -555.8486 RESTRAINT = 0.0000
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 40000 TIME(PS) = 50.000 TEMP(K) = 306.34 PRESS = 0.0
Etot = 222.0932 EKtot = 451.0901 EPtot = -228.9969
BOND = 116.2790 ANGLE = 351.3472 DIHED = 469.2875
1-4 NB = 118.3938 1-4 EEL = 1474.4917 VDWAALS = -165.3935
EELEC = -2042.9887 EGB = -550.4139 RESTRAINT = 0.0000
------------------------------------------------------------------------------
Any comments would be greatly appreciated.
Many thanks and Best Regards,
Moitrayee
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Received on Tue Apr 09 2013 - 19:00:03 PDT
