RE: PMEGridSize

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Thu Jul 23 2009 - 15:13:03 CDT

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

 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 MTStimestep               
 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                    

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 
      
     
    
       
    
    
    
    
    
    
    
   
  
     
  
  

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