From: Bylund, Tatsiana (NIH/NIAID) [F] (tatsiana.bylund_at_nih.gov)
Date: Tue Jan 12 2016 - 16:55:09 CST
Dear all,
I need to restart my run. The initial *.namd file
### Docking -- Step 1
set PSFFILE ionized.psf
set PDBFILE ionized.pdb
set GRIDPDB ionized-grid.pdb
set DIEL 1
set SCALING_1_4 1.0
set ITEMP 300
set FTEMP 300
set GRIDFILE CAP248-grid-trimmed.dx
set GSCALE 0.3
set EXTRAB {ionized-extrabonds.txt ionized-extrabonds-cispeptide.txt ionized-extrabonds-chirality.txt}
set CONSPDB 0
set FIXPDB 0
set OUTPUTNAME adk-solvent-step1
set TS 4000000
set MS 200
set MARGIN 0
####################################
structure $PSFFILE
coordinates $PDBFILE
paraTypeCharmm on
parameters par_all27_prot_lipid_na.inp
parameters PCA.inp
if {[info exists INPUTNAME]} {
BinVelocities $INPUTNAME.restart.vel
BinCoordinates $INPUTNAME.restart.coor
ExtendedSystem $INPUTNAME.restart.xsc
} else {
temperature $ITEMP
cellBasisVector1 215.6569938659668 0 0
cellBasisVector2 0 223.80899810791016 0
cellBasisVector3 0 0 194.74199676513672
cellOrigin 147.0274200439453 159.85952758789063 163.3546142578125
}
PME yes
PMEGridSpacing 1.0
PMEPencils 1
wrapAll on
source mdff_template.namd
####################################
In order to restart the run do I just need to set
set INPUTNAME name to "adk-solvent-step1" and change OUTPUTNAME to a new one, for ex. "adk-solvent-step1-r1"
Is there anything else I need to change?
Thank you!
Kind regards,
Tatsiana
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