[gmx-users] water molecules suffer from very long bond lengths

[sarbani chattopadhyay]

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                                                                                                              
~                                                                                                              
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