manjula kasinathan wrote:
hi all
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
pre-processor
Not that this matters (since cpp is ignored in Gromacs 4.0.x and would have
caused a serious error in the 3.3.x series), but Gromacs does not distribute a
cpp, so this line is nonsense. Just FYI.
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 this
And what was the output from the energy minimization? Are the resulting
potential energy and maximum force acceptable? Have you checked the output
configuration from any unresolved clashes?
-Justin
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
Cheers,
Manjula Kasinathan.
--
========================================
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
========================================
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