[gmx-users] Problem with CGMD

Anirban Ghosh reach.anirban.ghosh at gmail.com
Fri Oct 30 14:36:58 CET 2009


Hi ALL,

Thanks Justin for your reply.
Now after solvating my CG system of protein in lipid bilayer, I did EM and
the final energy values were reasonable. But while running MD I am getting
the following error:

-----------------------------------------------------------------------------------
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed
-----------------------------------------------------------------------------------

In the archives I found this error and possible solution "to check the
structure". But that is for all-atom system and according to  me my CG
system is OK. But I am not sure about the mdp parameters that I got from a
example script from MARTINI site for running lipid MD. So can you please
check the mdp file and suggest a solution for this problem.
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;

; VARIOUS PREPROCESSING OPTIONS =
title                    = Martini
cpp                      = /usr/bin/cpp

; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.

integrator               = md
; start time and timestep in ps
tinit                    = 0.0
dt                       = 0.030
nsteps                   = 900000
; number of steps for center of mass motion removal =
nstcomm                  = 1
comm-grps         =

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 1000
nstenergy                = 1000
; Output frequency and precision for xtc file =
nstxtcout                = 1000
xtc_precision            = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps                 =
; Selection of energy groups =
energygrps               =

; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.

; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.

; Method for doing electrostatics =
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r                = 15
; Method for doing Van der Waals =
vdw_type                 = Shift
; cut-off lengths        =
rvdw_switch              = 0.9
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.

; Temperature coupling   =
tcoupl                   = Berendsen
; Groups to couple separately =
tc-grps                  = Protein DSPC W
; Time constant (ps) and reference temperature (K) =
tau_t                    = 0.3 0.3 0.3
ref_t                    = 315 315 315
; Pressure coupling      =
Pcoupl                   = berendsen
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 3.0
compressibility          = 3e-5
ref_p                    = 1.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = no
gen_temp                 = 315
gen_seed                 = 666

; OPTIONS FOR BONDS     =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.

constraints              = none
; Type of constraint algorithm =
constraint_algorithm     = Lincs
; Do not constrain the start configuration =
unconstrained_start      = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order              = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle          = 30
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Any suggestion is welcome.

Regards,

Anirban
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