Re: PMEGridSize

From: V.Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Fri Oct 10 2008 - 09:49:12 CDT

try setting fullElectFreq to 1
Victor

PS your shake tolerance is a bit high, in my opinion.

On Fri, 2008-10-10 at 06:32 -0700, Rabab Toubar wrote:
> Thanks Chris for your reply,
>
> Below is my configuration file for the equilibration step. It is worth
> mentioning that I tried increasing the PMEGridsize and that's when my
> equilibration went fine. Visualizing the result using VMD, my molecule
> is leaving the solvation box completely.
>
> Any suggestions for what could be wrong?
> Thanks
> Rabab
>
> --------------------
> # input topology and initial structure..............
> structure dfn_solv.psf
> coordinates ./output/dfn_heat.coor
>
> #..force field block ........................
> paratypecharmm on
> parameters par_all22_prot.inp
> exclude scaled1-4
> 1-4scaling 1.0
> dielectric 1.0
>
> # dealing with long-range interactions..............
> switching on
> switchdist 8.0
> cutoff 12.0
> pairlistdist 13.5
> margin 0.0
> stepspercycle 20
> rigidBonds all
> rigidTolerance 0.00001
> rigidIterations 100
>
> # this block specifies the Ewald electrostatics.........................
> PME on
>
> PMETolerance 0.000001
>
> PMEGridSizeX 32
> PMEGridSizeY 32
> PMEGridSizeZ 32
>
> #block specifying the parameters for integrator and MTS
> timestep 1.0
> fullElectFrequency 4
>
> # this block specifies the output....
> outputenergies 1000
>
> outputtiming 1000
>
> binaryoutput no
> outputname output/dfn_equil
>
> restartname output/dfni_equil
> restartfreq 10000
> binaryrestart yes
> DCDfile output/dfn_equil.dcd
> dcdfreq 1000
> #MD protocol block ......................
> seed 1551
> numsteps 4000000
> temperature 300
>
> rescaleFreq 1
> rescaleTemp 300
>
>
> # this block defines periodic boundary conditions......
> cellBasisVector1 37.0 0.0 0.0
> cellBasisVector2 0.0 31.0 0.0
> cellBasisVector3 0.0 0.0 30.3
> cellOrigin 0.0 00.0 0.0
> wrapWater on
>
>
> --- On Fri, 10/10/08, Chris Harrison <char_at_ks.uiuc.edu> wrote:
>
> From: Chris Harrison <char_at_ks.uiuc.edu>
> Subject: Re: namd-l: PMEGridSize
> To: rtoubar_at_yahoo.com
> Cc: namd-l_at_ks.uiuc.edu
> Date: Friday, October 10, 2008, 1:37 AM
>
> Rabab,
>
> Post your namd configuration file. You have an energy leak.
> Assuming your system (the initial structure) is not
> pathological, we'll need to see your simulation parameters to
> judge the leak's cause.
>
> And to clarify, *what* "went through to the end"? The
> equilibration simulation or the entire protocol of
> simulations?
>
> Chris
>
>
>
> On Mon, Oct 6, 2008 at 10:51 AM, Rabab Toubar
> <rtoubar_at_yahoo.com> wrote:
> I do the minimization, heating and then equilibration
> steps separately before the simulation step. All ran
> fine apart from the simulation step that terminated
> without any error messages after may be 1/3 the
> simulation time. I had 2 suggestions: 1- PMEGridsize
> is too small and need to be > CellBasisVector (and
> this is mentioned in the tutorial) - 2 - the system
> didn't equilibrate ..so I need to run the
> equilibration step long enough.
>
> Adjusting the PME Gridsize and rerunning the
> simulation, it went through to the end BUT plotting
> the Total Energy vs TS showed a sharp decrease when it
> is supposed to be constant.
>
> Any suggestions?
> Thanks
> Rabab
>
> --- On Fri, 10/3/08, JC Gumbart <gumbart_at_ks.uiuc.edu>
> wrote:
> From: JC Gumbart <gumbart_at_ks.uiuc.edu>
>
> Subject: Re: namd-l: PMEGridSize
> To: rtoubar_at_yahoo.com
>
> Cc: "Roman Petrenko" <rpetrenko_at_gmail.com>,
> tutorial-l_at_ks.uiuc.edu, namd-l_at_ks.uiuc.edu
> Date: Friday, October 3, 2008, 10:53 PM
>
>
>
> Many shortcuts are taken in the NAMD tutorial
> simulations in the interest of speed; I'm not
> sure how much the PME grid size affects speed
> though (you could check yourself if
> interested). Therefore, what's written in the
> tutorial is much more important than what's in
> the configuration files themselves. While the
> simulation may appear to run fine with a
> coarse PME grid for a while, it's not
> accurate.
>
>
> Regarding why your simulation terminated
> unexpectedly, you will need to give us more
> information to determine that.
>
>
> On Oct 3, 2008, at 3:22 PM, Rabab Toubar
> wrote:
>
> > So you are suggesting leaving the Grid Size
> > as (32s) is and doing this gradual heating?
> >
> > Thanks Roman,
> > Rabab
> >
> > --- On Thu, 10/2/08, Roman Petrenko
> > <rpetrenko_at_gmail.com> wrote:
> >
> > From: Roman Petrenko
> > <rpetrenko_at_gmail.com>
> > Subject: Re: namd-l: PMEGridSize
> > To: rtoubar_at_yahoo.com
> > Cc: tutorial-l_at_ks.uiuc.edu,
> > namd-l_at_ks.uiuc.edu
> > Date: Thursday, October 2, 2008,
> > 4:22 PM
> >
> > gradual heating solved similar problem in my case. put this at the end
> > of your namd.conf script:
> > -----------------------------------------------------------------------------------------
> > set temperature 310
> >
> > set minimize_steps 300
> > set run_steps 10000000
> > #############################################################
> > ## EXECUTION SCRIPT ##
> > #############################################################
> >
> >
> > # Minimization
> > minimize $minimize_steps
> > reinitvels $temperature
> >
> > for {set i 25} {$i < $temperature} {incr i 25} {
> > set tempr $i
> > langevinTemp $tempr
> > reinitvels $tempr
> > run 100
> >
> > }
> >
> > firsttimestep 0
> > langevinTemp $temperature
> > run $run_steps
> >
> >
> >
> > On Thu, Oct 2, 2008 at 2:55 PM, Rabab Toubar <rtoubar_at_yahoo.com> wrote:
> >
> > >
> > Hi,
> > >
> > > In the namd tutorial it says on page 24: " Typically, a grid
> > size
> > > slightly less than 1 is a good
> > > A
> > > choice to reproduce charge distribution in biological systems,
> >
> > > where the closest atoms have a bond separation on the order of 1
> > > A. Furthermore, for speed in computing Fast Fourier Transforms,
> > > PMEGridSizeX should be chosen so that it can be factorized by
> > > 2, 3, or 5. If your cellBasisVector1 = (60, 0, 0), a good
> >
> > > choice for PMEGridSizeX might be 64, since 60 A/ 64 = 0.9375
> > > A and 64 = 26."
> > >
> > > While in the namd tutorial they used gridsizes of 32 in each direction
> > when
> > > the cellBasisVector was 42, 44 and 47, yet the simulation went OK.
> >
> > >
> > > I am asking this as I was running a simulation of cellBasisVector around
> > 35
> > > in each direction, and the gridsizes were
> > set to 32s according to the
> > > tutorial. I have been looking for the reasons of the unexpected
> > termination
> > > of the simulation. And according to the tutorial this couldn't be one.
> > >
> > > * My question is, how far could the PMEGridSizes affect the simulation?
> >
> > > * And if the equilibration step wasn't long enough, could this
> > terminate the
> > > simulation before completion?
> > >
> > > Thanks
> > > Rabab
> > >
> > >
> >
> >
> >
> > --
> > Roman Petrenko.
> >
> > Physics Department
> > University of Cincinnati
> >
>
>
>
>
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice:
> 217-244-1733
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
>
>

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