RE: PMEGridSize

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Oct 11 2008 - 14:44:16 CDT

There's no need to use shake (rigidbonds) with a 1 fs timestep. See the
description of multiple time stepping here:
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node26.html#SECTION0008370000000
0000000

Also, I guess the NAMD tutorial will discuss in detail as well along with
sample parameters.

As was alluded to below, the multiple time stepping algorithm does not
conserve energy exactly, although I'm not sure it would cause a sharp drop.
Try it (fullElectFreq 1) to see if this eliminates your problem (keeping in
mind your simulation will run slower then). Additionally, your switch
distance is too low; it should be 10 A, not 8. The namd manual gives a
pretty good description of what this is and what it should be set to.

Regarding the protein leaving the box, this could just be the natural
diffusion, combined with how VMD wraps molecules around periodic boundaries.
Presumably, there is a hole on the side of the box opposite to where the
protein is?

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of V.Ovchinnikov
Sent: Friday, October 10, 2008 9:49 AM
To: rtoubar_at_yahoo.com; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: PMEGridSize

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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