Re: pairlist i_upper mismatch!

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Sat Nov 22 2008 - 00:41:08 CST

hi,
just a remark/question:
why you are using a margin of 50?!
is it really necessary? usually, it should not.
Another thing, I saw: you are restarting velocities, but
the loop at the end does reset the thermostat (but not the velocities).
Is this behavior intended or do I miss something?
Finally, there is a line

> cutoff 12.switching on

Is it just a typo in the mail, or is the line really like that?

Same, in

> timestep 2.0 ;# 2fs/steprigidBonds all

This one, could maybe mess up your structure after some integration
steps.

eddi

On Nov 22, 2008, at 12:20 AM, Diego Alejandro Vargas wrote:

> Peter,
> I couldn't find any atoms that had the same coordinates. In VMD
> everything looks normal, and having checked all coordinates in
> the .pdb file no atoms show up within 0.5A or less of each other.
>
> Do you have any other idea of why I may be getting this error
> message? I am pasting my configuration file below in case it may be
> of help.
>
> Thank you,
> Diego
> ____________________________________________________________
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure /wt_fascin_wb.psf
> coordinates /wt_fascin_wb.pdb
> bincoordinates /wt_fascin_wb_mn.restart.coor
>
> binvelocities /wt_fascin_wb_mn.restart.vel
>
> extendedSystem /wt_fascin_wb_mn.restart.xsc
>
> set temperature 310
> set outputname ***
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ../common/par_all27_prot_lipid.inp
>
>
> # Force-Field Parametersexclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/steprigidBonds all
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
> margin 50.0
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp 1
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> # extendedSystem used.
>
> wrapAll on
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 100
> PMEGridSizeY 128
> PMEGridSizeZ 100
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp 1
>
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Gradual temperature increase:
> run 500
> for {set i 10} {$i <= $temperature} {incr i 10} {
> langevinTemp $i
> langevinPistonTemp $i
> run 500
> }
>
> run 250000 ;# 500ps

=====================================================
Eduard Schreiner
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
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================

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