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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Received on Tue May 18 2010 - 07:30:03 PDT
