[email protected] wrote:
Hi,
I am trying to run a simulation with 1360 Tip4p water molecules and one
methane molecule (Box size: 35.500 35.3371 35.500 and Total 5541 atoms)
but I am getting the error:
t = 0.000 ps: Water molecule starting at atom 5433 can not be settled.
Check for bad contacts and/or reduce the timestep.
Have you done sufficient energy minimization? General information can be found
within the wiki pages of the Gromacs site, i.e.:
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
-Justin
Here is my grompp. file :
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.002
nsteps = 25000
; number of steps for center of mass motion removal =
nstcomm = 1
ENERGY MINIMIZATION OPTIONS
emtol = 10000
emstep = 0.01
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 1000
nstvout = 1000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 0
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 100
xtc_precision = 1000
; This selects the subset of atoms for the xtc file. =
; Only the first group gets written out, it does not make sense =
; to have multiple groups. By default all atoms will be written =
xtc_grps =
; Selection of energy groups =
energygrps = CH4 SOL
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 1.0
; ns algorithm (simple or grid) =
ns_type = grid
; nblist cut-off =
rlist = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulomb_type = pme
rcoulomb_switch = 0
rcoulomb = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 1.0
epsilon_rf = 0
; Method for doing Van der Waals =
vdw_type = Cut-off
; cut-off lengths =
rvdw_switch = 0
rvdw = 1.0
dispcorr = enerpres
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = v-rescale
; Groups to couple separately =
tc-grps = system
; Time constant (ps) and reference temperature (K) =
tau_t = 0.1
ref_t = 300
; Pressure coupling =
Pcoupl = Berendsen
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0
compressibility = 4.6e-5
ref_p = 1
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 300
gen_seed = 171533
I am new to this, so any inputs would be appreciated.
Thanks
Nisha
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
