Hi Senthil,
This doesn't look very converged to me. There is a distinct curve in your
density, pressure and volume plots. Plus if you have formed vacuum bubbles
they can take a long time to equilibrate out. I would suggest running a
nanosecond or so of NTP (with taup=1.0) and then see what things look like.
Remember you are plotting average density, not local density so this won't
necessarily tell you that the bubbles have gone away.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Senthil Natesan
> Sent: Monday, May 17, 2010 12:12 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] solvent MD - poor equilibration
>
> 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 - 13:30:05 PDT
