[gmx-users] position restraints

[gadies at fh.huji.ac.il]

Hello,

I'm trying to run a simulation with one lipid molecule in a fixed
simulation box without pbc.
I set position restraints on one of the atoms and I seem to keep on
getting the following error:

"...This usually means your system is exploding..."

Do you have any idea what may cause this problem?
Not without further details.  Where did you get the parameters for your lipid?
What lipid is it?  What did you do to minimize and equilibrate your system?
What's in your .mdp file?

See here: http://wiki.gromacs.org/index.php/blowing_up

-Justin


Hello,

The lipid is DPPC.The .itp file I got from a coworker that used it  
before for membrane MD simulations.
To minimize the system I used steepest descent with the following parameters:
title = TAT
cpp = /usr/bin/cpp
define = -DPOSRE
constraints = none
integrator = steep
dt = 0.002 ;ps
nsteps = 400
nstlist = 10
ns_type = grid
rlist = 0.99
coulombtype = PME
rcoulomb = 0.99
vdwtype = cut-off
rvdw = 0.99
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
emtol = 1000.0
emstep = 0.01

I tried running the steepest descent several times however that did not help.
I run an MD simulation with the following parameters:
title = dppc
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.001 ;ps
nsteps = 100000
nstcomm = 1
nstxout = 1000
nstvout = 0
nstfout = 0
nstenergy = 1000
nstlist = 10
pbc = no
ns_type = simple
rlist = 1.4
coulombtype = cut-off
rcoulomb = 1.4
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Tcoupl = berendsen
tau_t = 1.0
tc-grps = DPP
ref_t = 300
Pcoupl = no
gen_vel = yes
gen_temp = 300.0
gen_seed = -1
bd_fric = 0
ld_seed = -1
epsilon_r = 80
comm_mode = angular

thank you
Gadi


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