From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue May 21 2013 - 01:02:42 CDT
Hi,
additionally, you only minimize your system for 100 steps. Check your out
file with VMD->Namd Plot to see if the TOTAL energy is near to converge, I
guess not, by far. So if you start the md in vacuum with lots degrees of
freedom and a barely minimized structure, in addition with 310K and a 2fs
timestep, it's not really surprising that your structure blows apart. The
rattle algorithm just tells you that a hydrogen moved too far away from it's
mother atom to constrain it back within the default iterations and
tolerance, this has nothing to do with the rigidbonds algorithm, it's just
the 1st thing to break. Turning of rigid bonds would turn into the message
"Atoms moving too fast". Try more minimization steps (about 1000 or more)
and if that doesn't completely solve it, reduce the timestep to default 1fs
at least for the equilibration.
Good luck
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Aron Broom
Gesendet: Dienstag, 21. Mai 2013 04:38
An: Corey Fugate
Cc: namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: Help with "ERROR: Constraint failure in RATTLE
algorithm for atom XXXX!"
so one key thing I note here is that you still have the langevinPiston on
and other things listed under "# Constant Pressure Control (variable
volume)". Since you are in a vacuum, this makes no sense, particularly the
attempt to set the pressure to 1 atm.
I would comment out all of that.
Also, the NAMD manual does a good job of describing all the parameters.
On Mon, May 20, 2013 at 6:28 PM, Corey Fugate <coreyfugate_at_gmail.com> wrote:
Aron, thanks for the suggestions. I have little idea how to implement the
suggestions you've made. I hate to do this, but my config file is below.
Can you show me where to make changes?
Thanks!!!!
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# LAM-protein only
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure lamA.psf
coordinates lamA.pdb
set temperature 310
set outputname lamA_eq
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
#cellBasisVector1 50.0 0. 0.0
#cellBasisVector2 0.0 50.0 0.0
#cellBasisVector3 0.0 0 50.0
#cellOrigin -27.4 2.7 -17.1
#wrapAll on
# PME (for full-system periodic electrostatics)
#PME yes
#PMEGridSpacing 1.0
#manual grid definition
#PMEGridSizeX 45
#PMEGridSizeY 45
#PMEGridSizeZ 48
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 100
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 100
reinitvels $temperature
run 2500 ;# 1ps
On Mon, May 20, 2013 at 1:07 PM, Aron Broom <broomsday_at_gmail.com> wrote:
tragic.
and you say that atom doesn't appear weird when visualizing? Are you
recording the DCD every timestep so you can catch the frame just before the
failure?
Maybe try being extreme in your energy minimization beforehand, as in 10,000
steps or something.
Also, are you gradually heating? I usually just initialize to 300K, but if
you are having problems, maybe do a slow heating of 1K per 1000 steps or
something. Are you using a Langevin thermostat?
On Mon, May 20, 2013 at 12:57 PM, Corey Fugate <coreyfugate_at_gmail.com>
wrote:
Good point. I commented out the lines in the configuration concerning
periodic boundary conditions and PME. The run fails with the same error
messages, but caused by different atoms.
On Mon, May 20, 2013 at 10:16 AM, Aron Broom <broomsday_at_gmail.com> wrote:
you should not have a box if you are doing vacuum simulations.
you need to not use periodic conditions and not use PME.
ideally pairdist and cutoff would be essentially infinite.
not sure if it is the problem, but when you use periodic conditions in a
vacuum, you have two issues:
1) PME doesn't work, because you don't have uniform density
2) if your system has a net charge, you are simulating an infinite lattice
of similarly charged systems which is madness
~Aron
On Mon, May 20, 2013 at 12:08 PM, Corey Fugate <coreyfugate_at_gmail.com>
wrote:
I am trying to minimize and equilibrate a protein monomer that consists of
6525 atoms (protein only). I am doing this is vacuum. I receive the
following error in my log file -
REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN
TCL: Running for 2500 steps
ERROR: Constraint failure in RATTLE algorithm for atom 1917!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
This seems to be a common question on the mailing list, so I first read
through some suggestions described previously. I've tried increasing the
cutoff and the pairlistdist. This didn't seem to help. It did change the
atom that seemed to cause the problem, it always seems to be to near the
surface f the protein. I looked at the pdb in VMD and I don't see any
unfavorable overlap between this atom and another. Jim Phillips mentioned
that a good rule of thumb is 1 atom per 10 cubic angstroms. I am working
with a box with periodic boundary conditions. If I have 6525 atoms, I would
need a box that had a volume of 65,250 A^3. The original dimensions of my
box set by the cellBasisVectors are 47,42,44. This would give me a box with
an area of 80,856 A^3. I went ahead and make the box larger by making all
the dimensions 50.
Am I missing something obvious? Any suggestions would be great.
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo -- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo -- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:13 CST