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<div>In God We Trust
<br />Hello Dear GMX users
<br />I want to do MD on one peptide in water with gromacs 4.5.3.
<br />I minimized and equilibrated my system in NPT and NVT for 50 ps , but
when I do final mdrun it has load imbalance and when I try -pd option
it stops after 265 ps without any error massage !, can everybody
help me.
<br />Here is my mdp file .
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<div>constraints =
hbonds
<br />integrator
= md
<br />
dt
= 0.002
<br />
nsteps
= 50000000
<br />
nstcomm
= 10
<br />
comm_mode
= Linear
<br />
comm_grps
= protein
<br />
nstxout
= 250
<br />
nstvout
= 1000
<br />
nstfout
= 0
<br />nstcalcenergy = 10
<br />
nstlog
= 1000
<br />
nstenergy
= 1000
<br />
nstlist
= 10
<br />
ns_type
= grid
<br />
rlist
= 1.2
<br />coulombtype =
PME
<br />
rcoulomb
= 1.2
<br />
rvdw
= 1.4
<br />fourierspacing = 0.12
<br />fourier_nx
= 0
<br />fourier_ny
= 0
<br />fourier_nz
= 0
<br />
pme_order
= 4
<br />ewald_rtol
= 1e-5
<br />optimize_fft = yes
<br />energygrps =
protein SOL
<br />
<br />
<br />; Berendsen temperature coupling is on in three groups
<br />
Tcoupl
= v-rescale
<br />
tau_t
= 0.1
1
<br />tc-grps = protein
bulk
<br />
ref_t
= 300
300
<br />; Pressure coupling is on
<br />
Pcoupl
= parrinello-Rahman
<br />
tau_p
= 1
<br />compressibility = 4.5e-5
<br />
ref_p
= 1.0
<br />; Generate velocites is on at 300 K.
<br />
gen_vel
= yes
<br />
gen_temp
= 300.0
<br />
gen_seed
= 173529
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<br />Many thanks in advance for your help and your reply.
<br />Yours truly
<br />Karim Mahnam
<br />Institute of Biochemistry and Biophysics (IBB)
<br />Tehran University
<br />P.O.box 13145-1384
<br />Tehran
<br />Iran
<br /><a href="http://www.ibb.ut.ac.ir/">http://www.ibb.ut.ac.ir/</a>
<br />
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