Thanks for the insights. I will try to run longer simulation. The reason I opted for truncated octahedron over rectangular box is
to avoid adding ~3000 additional water molecules. Already the system has ~28000 atoms and I am finding difficulty
in creating input file for Gaussian ONIOM calculation.
Yes I used "image familiar" while re imaging the coordinates using ptraj. I took the screen shot to give just an idea of
how the system looks after equilibration.
I agree with Ross on the lack of convergence. For point of reference, I simulate very small systems (short peptides) and equilibrate for anywhere from 100 ps to 1 ns at constant pressure.
Senthil, you also mentioned that you are using a truncated octahedral box. What does your ptraj script for imaging look like? Are you using "image familiar"? (The experts on this list can give you the definitive answer here, but I think you need the familiar tag when imaging systems with truncated octahedral boxes.) I ask because it looks like your box was sort of cubic in the screenshot you sent...
Paul
On May 17, 2010, at 1:26 PM, Ross Walker wrote:
> 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 - 16:00:06 PDT
