hi ,
i am trying to use GROMACS to perform MOLECULAR DYNAMICS simulation on a
small
peptide.
i gave the dimensions -d 0.75 in the 'editconf' command and then solvated the
box and
energy minimized it using 'l-bfgs' minimization process.
i ran a simulation for 10 ps, but the trajectory shows that the water molecules
at the surface
are suffering from unusually long bond lengths.The '.mdp' file i used is as
follows
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 10 ps.
nstcomm = 1
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
nstxtcout = 250 ; frequency to write coordinates to 'xtc' trajectory
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein SOL
tau_t = 0.1 0.1
ref_t = 300 300
; Energy monitoring
energygrps = Protein SOL
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 300 K.
gen_vel = no
gen_temp = 300.0
gen_seed = 173529
~ i am new to this field. any kind of suggestion is welcome
~
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
