VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Wed Jul 30 2003 - 07:53:39 CDT

Dear fellows,
 If you have some experience with namd could somebody explain why this
is happening (see error message at the bottom of the message)? I am
using the following script:. It is a constant pressure equilibration
using Berendsen algorithm for temp and pressure. This equilibration step
follows after a minim and a const Vol. eq in which the temperature is
adjusted to 300 (also with temp coupling scheme). The protocol below
works fine in AMBER but maybe there some differences between the values
used by the 2 programs that I didnt figure out. The first eq. at const
Vol works fine both in Amber and Namd so I guess there is something
about pressure here. If you want more details please let me know!.
  I would appreciate any advice. Thank you very much ,
Vlad

# *** AMBER force field *** ---------------------------------
amber on
parmfile rnaWI.top
coordinates rnaWI_mdeq2.pdb.coor
readexclusions yes
exclude scaled1-4
1-4scaling 0.83333333 #=1/1.2
scnb 2

#*** approximations for nonbonded interactions ------------
switching off
cutoff 9
stepspercycle 1

#***equilibration parameters
minimization off
numsteps 10000
timestep 1.0

#***SHAKE use
rigidbonds all

#***temperature regulation for equilibration step (NPT) using
#***temperature coupling
temperature 100.0
tcouple on
tcoupletemp 300.0
tcouplefile rnaWI_ceq2.pdb ### friction coef.=1.0
tcouplecol B

#***constant pressure equilibration using Berendsen bath coupling
usegrouppressure on
useflexiblecell on
berendsenpressure on
berendsenpressuretarget 1.0
berendsenpressurecompressibility 0.0000446
berendsenpressurerelaxationtime 500
berendsenpressurefreq 100

#***PME
PME on
cellBasisVector1 56.21 0 0
cellBasisVector2 0 58.53 0
cellBasisVector3 0 0 57.89
cellOrigin 0 0 0
PMEGridSizeX 50
PMEGridSizeY 55
PMEGridSizeZ 50
XSTfile rnaWI_mdeq3.XST
XSTfreq 200

#***constraints (holding the solute fixed)
constraints on
consexp 2
consref rnaWI_mdeq2.pdb.coor
conskfile rnaWI_res500.pdb
conskcol B

#***outputnames
outputname rnaWI_mdeq3.pdb
restartname rnaWI_mdeq3.rst
dcdfile rnaWI_mdeq3.dcd
dcdfreq 200
veldcdfile rnaWI_mdeq3.vel.dcd
veldcdfreq 200
restartfreq 200
outputenergies 100
outputpressure 100
binaryoutput off
binaryrestart off

###---error-----------------

RESSURE: 300 76798.7 -40631.2 58693.1 -13378.6 29200.3 -5152.76 69223.5
-42523.7 81493.1
GPRESSURE: 300 76687.2 -40836.2 58854.3 -13914.7 29538.5 -4262.26
68552.2 -42832.5 81484.6
ENERGY: 300 2002.7469 2400.4670 550.4454 0.0000
-61779.2755 9089.4231 60866.5902 0.0000 31247.2457 44377.6430
1056.1747 62497.3627 62570.0965 185386.7344 -1757.5130 -1600.7691
ERROR: Constraint failure in RATTLE algorithm for atom 121!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
========================================== 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204