[gmx-users] gromacs doubt
manjubfs at gmail.com
Thu May 13 09:42:32 CEST 2010
i have done protein protein interaction and the complex structure
was taken for MD simulation using Gromacs.while performing mdrun step for
position restrain i got error. i have carried out mdrun for 1ps and the
command given for mdrun
and position restrain are
grompp -f *.pdb -c *.gro -p top.top -o *.tpr
mdrun -v -deffnm pr
my em.mdp file
title = com
cpp = /usr/local/gromacs/share/gromacs/cpp ; the c
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 3000
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
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
; Energy minimizing stuff
emtol = 1000.0
emstep = 0.01.
here i have given nsteps 3000. but while doing energy minimization it
considers only 1000 steps and the energy was minimized for only 1000 steps.
then i gone for position restrain step while doing Mdrun i got error like
starting mdrun 'Protein in water'
500 steps, 1.0 ps.
step 400, remaining runtime: 132 s
Step 402, time 0.804 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000119, max 0.006712 (between atoms 2873 and 2875)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2873 2875 64.4 0.0989 0.1007 0.1000
t = 0.868 ps: Water molecule starting at atom 93766 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
wat should i do now. how can i progress this.could any one help me plz.
thank in advance
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