Job description

This section is needed are we trying to keep track of each run, please put type of simulation, pdb loaded, date, time and your name

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## JOB DESCRIPTION ##

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# NPT simul

# 2v0u in a water box

# 12.08.09

# 14:00

# Nicolas Gobet

Adjustable parameters

First run

This is an example for the heating.

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## ADJUSTABLE PARAMETERS ##

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structure ./2v0up_wb_i.psf

coordinates ./2v0up_wb_i.pdb

set paramfich ./common/par_all27_prot_lipid-fmn_dark.prm

set temperature 300

set outputdir ./output_eq3

set outputname $outputdir/2v0up_wb_i_eq

set outputmin $outputdir/min

set outputheating $outputdir/heating

set outputnpt1 $outputdir/NPT_1

set outputnvt $outputdir/NVT_1

set outputnpt2 $outputdir/NPT_2

Resume after previous complete run

This is to resume from .coor, .vel and .xsc files. As we load velocities and positions from a file, we don't have to set initial temperature, load .pdb for postions of the atoms and set parameters such as box size

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## ADJUSTABLE PARAMETERS ##

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structure ./2v0up_wb_i.psf

set paramfich ./common/par_all27_prot_lipid-fmn_dark.prm

set temperature 300

set inputdir ./output_eq2

coordinates $inputdir/2v0up_wb_i_eq.coor

velocities $inputdir/2v0up_wb_i_eq.vel

extendedSystem $inputdir/2v0up_wb_i_eq.xsc

set outputdir ./output_sim2

set outputname $outputdir/2v0up_wb_i_sim

set outputsim $outputdir/min