[gmx-users] problem with freeze-group : Large VCM

jagannath mondal jmondal2004 at yahoo.co.in
Fri May 11 01:19:53 CEST 2007

Hi Gromacs user,

     I am a gromacs beginner struggling with
freeze-group simulation.
 I was trying to simulate a beta-peptide(un-natural
peptide ) by relaxing only the side-chains but I am
getting error regarding large VCM and 
The system has only 1 peptide (14-residue ) and No
solvent.  So, for this purpose , I generated a
freeze-group which contains all the main-chain atoms.
Initially I was using pressure-coupling and it was
giving error in simulation.   Later   I found many
discussion on this freeze-group simulation in
user-archive and manual and  accordingly 
  I did not use pressure-coupling in my simulation 
and before the simulation, I minimised my peptide
using steep
 integrator and then  with the minimised structure I
tried a MD run. But after 40 ps, the mdrun crashes
with complaint about nsgrid and large VCM:
  Large VCM(group rest):   -290.48474,   -162.64799,  
 121.63662, ekin-cm:  9.32182e+07
Large VCM(group rest):   -282.17371,   -168.38831,   
148.67302, ekin-cm:  9.65194e+07
Large VCM(group rest): -1636559744.00000,
742081920.00000, 817249536.00000, ekin-cm: 
There were 6 inconsistent shifts. Check your topology
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each
particle to a grid
based on its coordinates. If your system contains
collisions or parameter
errors that give particles very high velocities you
might end up with some
coordinates being +-Infinity or NaN (not-a-number).
Obviously, we cannot
put these on a grid, so this is usually where we
detect those errors.
Make sure your system is properly energy-minimized and
that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been
within [ 0 .. 2352637 ]
Please report this to the mailing list
(gmx-users at gromacs.org)
I am giving my .mdp file used for simulation.

Can anyone help me in this respect or suggest some
change in mdp file. Is there anything wrong in my mdp
file and particularly  in centre of mass  part? Do I
need to do any position-restrained MD? If so, can
anyone explain me how to do that.
 Jagannath Mondal

integrator               = md
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.002
nsteps                   = 200000
; For exact run continuation or redoing part of a run
init_step                = 0
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                =
; This selects the subset of atoms for the xtc file.
You can
; select multiple groups. By default all atoms will be
xtc-grps                 =
; Selection of energy groups
energygrps               =

; nblist update frequency
nstlist                  = 5
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz (default), no
; or full (infinite systems only)
pbc                      = xyz
; nblist cut-off
rlist                    = 0.9
domain-decomposition     = no
; Method for doing electrostatics
coulombtype              = Cut-off
rcoulomb-switch          = 0
rcoulomb                 = 0.9
; Dielectric constant (DC) for cut-off or DC of
reaction field
epsilon-r                = 1
; Method for doing Van der Waals
vdw-type                 = Cut-off
; cut-off lengths
rvdw-switch              = 0
rvdw                     = 0.9
; Apply long range dispersion corrections for Energy
and Pressure
DispCorr                 = EnerPres
; Temperature coupling
Tcoupl                   = berendsen
; Groups to couple separately
tc-grps                  = System
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.1
ref_t                    = 300
; Pressure coupling
Pcoupl                   = no
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and
reference P (bar)
tau_p                    = 0.5
compressibility          = 4.5e-5
ref_p                    = 1.0
; Random seed for Andersen thermostat
andersen_seed            = 815131
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 1993

constraints              = none
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
unconstrained-start      = no
; Use successive overrelaxation to reduce the number
of shake iterations
Shake-SOR                = no
; Relative tolerance of shake
shake-tol                = 1e-04
; Highest order in the expansion of the constraint
coupling matrix
lincs-order              = 4
lincs-iter               = 1
; Lincs will write a warning to the stderr if in one
step a bond
; rotates over more degrees than
lincs-warnangle          = 30
; Convert harmonic bonds to morse potentials
morse                    = no
; Non-equilibrium MD stuff
acc-grps                 =
accelerate               =
freezegrps               = MainChain+Cb
freezedim                = Y Y Y
cos-acceleration         = 0

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