From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Jul 23 2009 - 16:52:06 CDT
You can, but the speed gain won't be x2, and you'll lack any energy term for
the hydrogens in your output. Any concerns over this should be taken in
context of the specific property you are trying to measure. Caveat emptor.
Chris
--
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
On Thu, Jul 23, 2009 at 3:13 PM, Rabab Toubar <rtoubar_at_yahoo.com> wrote:
> Hi,
> When there is no need to use Rigidbonds all with a 1 fs, "can" we use it?
> Just to decrease the computer cost and the simulation time.
> Thanks
>
> Rabab Toubar
>
>
> --- On *Sat, 10/11/08, 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, char_at_ks.uiuc.edu
> Cc: namd-l_at_ks.uiuc.edu
> Date: Saturday, October 11, 2008, 2:01 AM
>
>
> 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#SECTION00083700000000000000
>
>
>
> Also, I guess the NAMD tutorial will discuss in detail as well along with
> sample parameters.
>
>
>
> As was alluded to by Victor, 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) though 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?
>
>
>
>
>
> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *Rabab Toubar
> *Sent:* Friday, October 10, 2008 8:32 AM
> *To:* char_at_ks.uiuc.edu
> *Cc:* namd-l_at_ks.uiuc.edu
> *Subject:* Re: namd-l: PMEGridSize
>
>
>
> 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<http://mc/compose?to=rtoubar@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<http://mc/compose?to=gumbart@ks.uiuc.edu>
> >* wrote:
>
> From: JC Gumbart <gumbart_at_ks.uiuc.edu<http://mc/compose?to=gumbart@ks.uiuc.edu>>
>
>
>
> Subject: Re: namd-l: PMEGridSize
> To: rtoubar_at_yahoo.com <http://mc/compose?to=rtoubar@yahoo.com>
>
> Cc: "Roman Petrenko" <rpetrenko_at_gmail.com<http://mc/compose?to=rpetrenko@gmail.com>>,
> tutorial-l_at_ks.uiuc.edu <http://mc/compose?to=tutorial-l@ks.uiuc.edu>,
> namd-l_at_ks.uiuc.edu <http://mc/compose?to=namd-l@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<http://mc/compose?to=rpetrenko@gmail.com>
> >* wrote:
>
> From: Roman Petrenko <rpetrenko_at_gmail.com<http://mc/compose?to=rpetrenko@gmail.com>
> >
> Subject: Re: namd-l: PMEGridSize
> To: rtoubar_at_yahoo.com <http://mc/compose?to=rtoubar@yahoo.com>
> Cc: tutorial-l_at_ks.uiuc.edu <http://mc/compose?to=tutorial-l@ks.uiuc.edu>,
> namd-l_at_ks.uiuc.edu <http://mc/compose?to=namd-l@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 <http://mc/compose?to=rtoubar@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 <http://mc/compose?to=char@ks.uiuc.edu>
> Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
>
>
>
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