Thanks Bill, Paul and Carlos for your valuable suggestions. Now I ran 40 ps constant pressure
simulation with taup = 0.1 (after 20 ps constant volume run). I reimaged the .rst file and here is the output.
Please look at the snapshot of the complex and the arrow-pointed region. I am attaching all analysis
pictures.
Dr. Simmerling suggested me to check whether there is any bad force field parameters? can anyone
educate me how to do the same?
------------------------------------------------------------------------------
A V E R A G E S O V E R 80 S T E P S
NSTEP = 40000 TIME(PS) = 60.000 TEMP(K) = 300.32 PRESS = 1.6
Etot = -44706.7284 EKtot = 20935.9646 EPtot = -65642.6930
BOND = 13187.8322 ANGLE = 2153.6667 DIHED = 3131.7413
1-4 NB = 998.3376 1-4 EEL = 13428.8920 VDWAALS = 9418.6629
EELEC = -109086.9867 EHBOND = 0.0000 RESTRAINT = 1125.1611
EAMBER (non-restraint) = -66767.8541
EKCMT = 5617.2295 VIRIAL = 5608.3618 VOLUME = 256293.1378
Density = 0.9430
Ewald error estimate: 0.5938E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 40000 TIME(PS) = 60.000 TEMP(K) = 1.61 PRESS = 93.2
Etot = 238.6872 EKtot = 112.4630 EPtot = 196.7113
BOND = 114.6308 ANGLE = 38.0862 DIHED = 15.4679
1-4 NB = 11.4936 1-4 EEL = 25.6773 VDWAALS = 144.6216
EELEC = 267.1154 EHBOND = 0.0000 RESTRAINT = 47.2495
EAMBER (non-restraint) = 149.4617
EKCMT = 60.0166 VIRIAL = 522.8410 VOLUME = 2129.6454
Density = 0.0077
Ewald error estimate: 0.3859E-04
------------------------------------------------------------------------------
thanks so much..
Senthil
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Received on Mon May 17 2010 - 12:30:04 PDT
