Re: [AMBER] solvent MD - poor equilibration

From: Senthil Natesan <sen.natesan.yahoo.com>
Date: Mon, 17 May 2010 12:12:07 -0700 (PDT)

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
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