From: Brittany Morgan (brmorgan_at_clarku.edu)
Date: Thu Mar 05 2009 - 07:56:47 CST
Hi Chris,
Here is the psfgen input script:
topology /home/brittanym/topparnew/top_all27_p_n_new.inp
pdbalias residue HIS HSD
pdbalias atom MET H HN
pdbalias atom MET HB2 HB1
pdbalias atom MET HB3 HB2
pdbalias atom MET HG2 HG1
pdbalias atom MET HG3 HG2
pdbalias atom GLN H HN
pdbalias atom GLN HB2 HB1
pdbalias atom GLN HB3 HB2
pdbalias atom GLN HG2 HG1
pdbalias atom GLN HG3 HG2
pdbalias atom LYS H HN
pdbalias atom LYS HB2 HB1
pdbalias atom LYS HB3 HB2
pdbalias atom LYS HD2 HD1
pdbalias atom LYS HD3 HD2
pdbalias atom LYS HE2 HE1
pdbalias atom LYS HE3 HE2
pdbalias atom LYS HG2 HG1
pdbalias atom LYS HG3 HG2
pdbalias atom GLY H HN
pdbalias atom GLY HA2 HA1
pdbalias atom GLY HA3 HA2
pdbalias atom ASN H HN
pdbalias atom ASN HB2 HB1
pdbalias atom ASN HB3 HB2
pdbalias atom PHE H HN
pdbalias atom PHE HB2 HB1
pdbalias atom PHE HB3 HB2
pdbalias atom ARG H HN
pdbalias atom ARG HB2 HB1
pdbalias atom ARG HB3 HB2
pdbalias atom ARG HD2 HD1
pdbalias atom ARG HD3 HD2
pdbalias atom ARG HG2 HG1
pdbalias atom ARG HG3 HG2
pdbalias atom THR H HN
pdbalias atom ALA H HN
pdbalias atom VAL H HN
pdbalias atom CYS H HN
pdbalias atom CYS HB2 HB1
pdbalias atom CYS HB3 HB2
pdbalias atom GLU H HN
pdbalias atom GLU HB2 HB1
pdbalias atom GLU HB3 HB2
pdbalias atom GLU HG2 HG1
pdbalias atom GLU HG3 HG2
pdbalias atom HIS H HN
pdbalias atom HIS HB2 HB1
pdbalias atom HIS HB3 HB2
pdbalias atom ILE H HN
pdbalias atom ILE CD1 CD
pdbalias atom ILE HG12 HG11
pdbalias atom ILE HG13 HG12
pdbalias atom ILE HD11 HD1
pdbalias atom ILE HD12 HD2
pdbalias atom ILE HD13 HD3
pdbalias atom PRO HB2 HB1
pdbalias atom PRO HB3 HB2
pdbalias atom PRO HD2 HD1
pdbalias atom PRO HD3 HD2
pdbalias atom PRO HG2 HG1
pdbalias atom PRO HG3 HG2
pdbalias atom TRP H HN
pdbalias atom TRP HB2 HB1
pdbalias atom TRP HB3 HB2
pdbalias atom ASP H HN
pdbalias atom ASP HB2 HB1
pdbalias atom ASP HB3 HB2
pdbalias atom SER H HN
pdbalias atom SER HB2 HB1
pdbalias atom SER HB3 HB2
pdbalias atom SER HG HG1
pdbalias atom LEU H HN
pdbalias atom LEU HB2 HB1
pdbalias atom LEU HB3 HB2
pdbalias atom TYR H HN
pdbalias atom TYR HB2 HB1
pdbalias atom TYR HB3 HB2
segment VTS {pdb VTS_U.pdb; first NONE; last CTER; auto none}
coordpdb VTS_U.pdb VTS
writepsf VTSU.psf
writepdb VTSU.pdb
The NAMD configuration file:
structure /home/morganb/vtsu/vtsu.solv.psf
coordinates /home/morganb/vtsu/vtsu.solv.pdb
outputName ./min/vts.output
set temperature 298
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters /home/morganb/par_all27_p_n_new.inp
# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature
# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {1} {
cellBasisVector1 54. 0. 0.
cellBasisVector2 0. 54. 0.
cellBasisVector3 0. 0. 54.
cellOrigin 0.35 -0.93 1.59
}
wrapWater on
wrapAll on
zeroMomentum no ; #can use for NVE
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 0.5 ;# 2fs/step
#rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 10
#PME (for full-system periodic electrostatics)
if {1} { # For speed, grid sizes should only have factors of 2, 3 and 5
PME yes
PMEGridSizeX 54
PMEGridSizeY 54
PMEGridSizeZ 54
PMEGridSpacing 1.0
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}
restartfreq 2000 ;# 500steps = every 1ps
dcdfreq 100
xstFreq 2000
outputEnergies 100
outputPressure 100
#velDCDfreq 100
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
if {1} {
minimize 5000; # Number of force evaluations
reinitvels $temperature
}
run 0;
_____
From: charris5_at_gmail.com [mailto:charris5_at_gmail.com] On Behalf Of Chris
Harrison
Sent: Wednesday, March 04, 2009 8:41 PM
To: Brittany Morgan
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Minimization convergence issue
If you are using a script as input to psfgen, can you paste the script in a
reply email? Can you also paste the namd configuration file. Sounds like
something could be wrong with angle, vdW, etc definitions in the psf or
parameters read-in during NAMD's startup.
C.
-- Chris Harrison, Ph.D. 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 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:26 CST