Dear AMBER list,
How do I get this error at unrestrained NPT equilibration since I can load
and visualize in VMD the prmtop and .rst file from NVT equilibration?
The number of atoms in the .rst file is the same as in the .prmtop. Below
is the configuration file I used in NVT.
PS: the system contains a protein, 2 ligands, 1 CL- and SPC/E waters. I use
pmemd.cuda in every step.
Heating up the system equilibration stage 1 (NVT)
&cntrl
nstlim=10000, ! Number of MD-steps to be performed.
dt=0.002,
ntx=1, ! read coordinates but not velocities from the inpcrd file
irest=0, ! this is not a simulation restart
ntpr=100, ! print energy every 500 steps
ntwr=500, ! write restart file (.restrt) every 5000 steps
ntwx=500, ! save coordinates every 5000
ntb=1, ! use periodic boundary conditions
ioutfm=1, ! use binary NetCDF format for the coordinate and velocity
trajectory files (mdcrd, mdvel and inptraj).
! iwrap=1 does not work with NVT ! wrap coordinates into primary box
! TEMPERATURE CONTROL
tempi =100.0, ! If no initial velocities are provided, choose this as
the inital temperature.
temp0=310.0, ! reference temperature at which the system is to be
kept, if ntt > 0
ntt=3, ! Use Langevin thermostat.
gamma_ln=5, ! Damping coefficient for Langevin dynamics in ps - 1.
tautp=2.0, ! Time constant, in ps, for heat bath coupling for the
system, if ntt = 1
ig=-1, ! The seed for the pseudo-random number generator
! PRESSURE CONTROL
ntp=0, ! not pressure coupling
! BOND CONSTRAINTS
ntc=2, ! bonds involving hydrogen are constrained with SHAKE
tol=1.0e-8, ! Relative geometrical tolerance for coordinate resetting
in shake
jfastw=0, ! Use faster SETTLE instead of SHAKE for bonds belonging to
water molecules. Waters are identified by the default names
! ELECTROSTATICS & VDW
ntf=2, ! ommit force evaluations for bond interactions involving
H-atoms
nrespa=1, ! evaluate forces every step (only nrespa=1 supported by
pmemd.cuda)
cut=9, ! Cut-off for vdW and electrostatic interactions.
! RESTRAINTS
ntr=1, ! restrain specified atoms in Cartesian space using a
harmonic potential
ntrx=1, ! format of the Cartesian coordinates for restraint
from the refc file (0:binary,1:ASCII)
restraint_wt=200, ! the weight (in kcal=mol-Å^2) for the positional
restraints; a high value may be necessary
restraintmask=':1-372.CA,C,O,N,H', ! string that specifies the
restrained atoms (backbone atoms in residues 62-82,152-162 restrained)
&end
skinnb=2.0, ! Distance between pairs of atoms for inclusion in pair
lists that are used to calculate vdW and electrostatic interactions.
vdwmeth=1, ! Apply an analytical tail correction to the reported vdW
energy and virial that is equal to the amount lost due to switching and
cutoff
! of the LJ potential.
! nfft1=intx , nfft2=inty, nfft3=intz ! The size of the fftw grid on each
dimention.
dsum_tol=1.0e-6, ! PME direct space tolerance.
order=4, ! PME interpolation order.
netfrc=1, ! Remove center of mass drift due to PME.
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Sun Aug 18 2013 - 16:30:02 PDT
