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<BR>
hi ,<BR>
i am trying to use GROMACS to perform MOLECULAR DYNAMICS simulation on a small <BR>
peptide.<BR>
i gave the dimensions -d 0.75 in the 'editconf' command and then solvated the box and <BR>
energy minimized it using 'l-bfgs' minimization process.<BR>
i ran a simulation for 10 ps, but the trajectory shows that the water molecules at the surface <BR>
are suffering from unusually long bond lengths.The '.mdp' file i used is as follows<BR>
<BR>
cpp = /usr/bin/cpp<BR>
constraints = all-bonds<BR>
integrator = md<BR>
dt = 0.002 ; ps !<BR>
nsteps = 5000 ; total 10 ps.<BR>
nstcomm = 1<BR>
nstxout = 250<BR>
nstvout = 1000<BR>
nstfout = 0<BR>
nstlog = 100<BR>
nstenergy = 100<BR>
nstxtcout = 250 ; frequency to write coordinates to 'xtc' trajectory<BR>
nstlist = 10<BR>
ns_type = grid<BR>
rlist = 1.0<BR>
rcoulomb = 1.0<BR>
rvdw = 1.0<BR>
; Berendsen temperature coupling is on in two groups<BR>
Tcoupl = berendsen<BR>
tc-grps = Protein SOL<BR>
tau_t = 0.1 0.1<BR>
ref_t = 300 300<BR>
; Energy monitoring<BR>
energygrps = Protein SOL<BR>
; Isotropic pressure coupling is now on<BR>
Pcoupl = berendsen<BR>
Pcoupltype = isotropic<BR>
tau_p = 0.5<BR>
compressibility = 4.5e-5<BR>
ref_p = 1.0<BR>
; Generate velocites is off at 300 K.<BR>
gen_vel = no<BR>
gen_temp = 300.0<BR>
gen_seed = 173529<BR>
<BR>
~ i am new to this field. any kind of suggestion is welcome <BR>
~
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