RE: PMEGridSize

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Oct 11 2008 - 01:01:58 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 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> 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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