normal sample.mdp file for making input.tpr file in using g_membed

  • thu nguyen
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11 years 1 month ago - 11 years 1 month ago #1390 by thu nguyen
Dear All,

I set up sample.mdp file for making input.tpr in using g_membed to insert protein into membrane as follows:

integrator = md
tinit = 0.0
dt = 0.02
nsteps = 1000
init_step = 0
comm-mode = Linear
nstcomm = 1
comm-grps =
emtol = 2000
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 5000
nstenergy = 100
nstxtcout = 1000
xtc-precision = 100
energygrps = Protein
energygrp_excl = Protein Protein
nstlist = 10
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 1.2
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = Protein DSPC W
tau-t = 1.0 1.0 1.0
ref-t = 310 310 310
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau-p = 2.0 2.0
compressibility = 3e-04 3e-04
ref-p = 1.0 1.0
refcoord_scaling = No
andersen_seed = 815131
gen-vel = yes
gen-temp = 310
gen-seed = 173529
constraints = all-bonds
constraint-algorithm = Lincs
continuation = no
Shake-SOR = no
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
morse = no
freezegrps = Protein
freezedim = Y Y Y



Is there anything wrong in it ?
I do not have experience in using g_membed. I hope those who have more experience, will give useful advice.

Thanks so much for any help !
Regards,
KT

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11 years 1 month ago #1392 by djurre
You probably have better changes to get an answer if you ask this at the gromacs mailing list.

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11 years 2 weeks ago #1433 by xavier
We are indeed not familiar with this procedure.

Please let us know if you find the solution.

djurre wrote: You probably have better changes to get an answer if you ask this at the gromacs mailing list.

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