Hi Senthil,
My suggestion would be to give up trying to equilibrate out the vacuum
bubbles, they will have seriously distorted your protein anyway. I would go
back to the beginning, minimize and then heat to 100K in about 10ps. Then
immediately switch to NPT for the remainder of the heating and keep running
in NPT for about 1ns or so. This way you will avoid forming the vacuum
bubbles in the first place and life should be much less complicated.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Senthil Natesan
> Sent: Tuesday, May 18, 2010 7:17 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] solvent MD - poor equilibration
>
>
>
> Dr. Simmerling,
>
> Thanks. Yes I posted volume and density plots ( I am attaching here
> again) and people suggested that they
> don't see proper convergence (I wrote the output every 500 steps, I
> guess that is the reason for spikes)
> So I am running long simulations now with suggested parameters. As far
> as force field parameters, I am using standard Amber force
> fieldleaprc.ff02. For ligands, I used GAFF and there is no warning in
> the frcmod file.
> I will report here again once I finish the simulations.
>
> Senthil
>
>
>
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Mon, May 17, 2010 10:41:59 PM
> Subject: Re: [AMBER] solvent MD - poor equilibration
>
> first, plot volume and density vs time and see the profile. you can't
> check equilibration with a single snapshot.
> for force field, please tell us if the simulation is all standard
> Amber parameters, or if you created anything new.
>
>
> On Mon, May 17, 2010 at 3:12 PM, Senthil Natesan
> <sen.natesan.yahoo.com> wrote:
> > 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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> >
> >
>
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Received on Tue May 18 2010 - 09:00:04 PDT
