Re: Fwd: Majordomo results

From: Kuldeep Roy (kuldeepkroy_at_gmail.com)
Date: Wed Jan 01 2014 - 16:33:22 CST

*I think that directories containing input files (coor, psf, parameter etc)
is not correctly set.*
*Apart from ones indicated by Farzad, even parameter file is not correctly
set. *

parameters ./common/par_all27_prot_lipid.inp

*Setting these files correctly should lead to successful job run.*

On Wed, Jan 1, 2014 at 2:57 PM, farzad kiani <farzad_kiani1364_at_yahoo.com>wrote:

> " ../common/ap9_2_ws.psf" what is this???????!!!!!!!!!
> you have been set incorrect directories for your files. set them correctly
>
>
>
>
> On Wednesday, January 1, 2014 2:55 PM, Faezeh Mottaghitalab <
> faezeh.mt258_at_gmail.com> wrote:
> Hello
>
> I'm trying to simulate Bacteriorhodopsin with the NAMD 2.9 in unix.
> first of all i have been omitted the retinal group of the protein from the
> pdb file and i have gain the files for the 1-2 sphere, 1-3 box and 1-4
> gbis ( to explain better i preferred to write the steps same as tutorial
> file 'ubq').
>
> i'm now in the 2-4 temp step and the problem is i get error 'segmentation
> fault' in this step and can't understand what is the problem.
>
> first i guess that maybe the dcd , vel ,xsc files haven't been created
> correctly but i have tested again and again different namd-tutorial-files
> and get the same error (segmentation fault)!
>
> the pdb id of the bacteritodopsin that i'm using is : 1AP9
> and here is my configuration file :
>
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Equilibration of Ubiquitin in a Water Sphere
> # Use for calculating temperature fluctuations
> # WARNING: DOES NOT SAVE DCD (and normally you need it)
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ../common/ap9_2_ws.psf
> coordinates ../common/ap9_2_ws.pdb
>
> set temperature 310
> set outputname ap9_2-nve
>
>
> # Continuing a job from the restart files
> if {1} {
> set inputname ../1-2-sphere/ap9_2_ws_eq
> binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel ;# remove the "temperature"
> entry if you use this!
> extendedSystem $inputname.restart.xsc
> }
>
> firsttimestep 0
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ./common/par_all27_prot_lipid.inp
> #temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> if { 0 } {
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
> }
>
> # Output
> outputName $outputname
>
> #restartfreq 50 ;# 500steps = every 1ps
> #dcdfreq 50
> outputEnergies 50
> outputPressure 50
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> # Spherical boundary conditions
> sphericalBC on
> sphericalBCcenter 16.626047134399414, 39.246639251708984,
> 6.797718524932861
> sphericalBCr1 26.0
> sphericalBCk1 10
> sphericalBCexp1 2
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> # minimize 900
> # reinitvels $temperature
>
> run 5000 ;# 1000ps
>
> thanks in advance,
> faezeh
>
> ---------- Forwarded message ----------
> From: <majordomo_at_ks.uiuc.edu>
> Date: Wed, Jan 1, 2014 at 1:32 PM
> Subject: Majordomo results
> To: faezeh.mt258_at_gmail.com
>
>
> --
>
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