From: Tao Qu (qutao1125_at_gmail.com)
Date: Thu Jun 06 2013 - 15:04:56 CDT
---------- Forwarded message ----------
From: Tao Qu <qutao1125_at_gmail.com>
Date: Thu, Jun 6, 2013 at 12:16 PM
Subject: Fwd: NAMD tcouple atoms moving too fast
To: namd-l_at_ks.uiuc.edu
Hi,
I was running simulations with tcouple option in NAMD. I always got the
error of "atoms moving too fast" without minimization steps. It was running
well if I add the minimization steps. Can the minimization be used with the
tcouple option in NAMD?
Thank you very much.
Tao Qu
MY INPUT FILE:
structure tcl_final.psf
coordinates tcl_final.pdb
set temperature 300
set outputname tcl_300
firsttimestep 0
# Input
paraTypeCharmm on
parameters par_hap_charmm.inp
parameters par_all27_prot_lipid.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
vdwGeometricSigma yes
# Integrator Parameters
timestep 0.1 ;# 0.1fs/step
#rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 1
# Periodic Boundary Conditions
cellBasisVector1 18.8428 -32.6376 0.0
cellBasisVector2 37.6856 65.2734 0.0
cellBasisVector3 0.0 0.0 179.00
cellOrigin 0.0 0.0 0.0
COMmotion no ;# default is no
zeroMomentum yes
# PME (for full-system periodic electrostatics)
PME yes
#PMEGridSpacing 1.0
PMEGridSizeX 150
PMEGridSizeY 100
PMEGridSizeZ 250
if {1} {
constraints On
consref tcl_hot.pdb
consexp 2
conskfile tcl_hot.pdb
conskcol B
}
# this is to heat the collagen
if {1} {
tCouple on
tCoupleTemp 200
tCoupleFile tcl_hot.pdb
tCoupleCol B
}
# Minimization
#minimize 5000 ;# 5 ps
#reinitvels $temperature
run 50000 ;# 50 ps
THE ERROR:
ERROR: Atom 21460 velocity is 39184.6 -1.70846e+06 -41472.9 (limit is
120000, atom 242 of 327 on patch 26 pe 0)
ERROR: Atom 22596 velocity is -470454 -273254 -12085 (limit is 120000, atom
315 of 327 on patch 26 pe 0)
ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on
patch 26 pe 0).
ERROR: Atom 16321 velocity is -2.73103e+06 -1.14559e+06 -3.53751e+06 (limit
is 120000, atom 78 of 302 on patch 27 pe 0).......
ERROR: Exiting prematurely; see error messages above.
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