[gmx-users] frezzing a bond : NPT and NVT simulations

[Nilesh Dhumal]

Hello
I am trying to constraints of a bond. I checked the distance using g_dist,
distance changes from 3.5 A to ~ 8.0A.
Can anyone tell why it changes.
Here I have pasted mdp file and itp file.
Nilesh
Solvent.itp
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
;1               3               yes             0.5     0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
;  name  bond_type    mass    charge   ptype          sigma      epsilon
  opls_997   PA 0   100.0000    1.000       A    0.40000e-01  0.82890e-01
  opls_998   NE 0   100.0000   -1.000       A    0.40000e-01  0.82890e-01

[ bondtypes ]
; i    j  func       b0          kb
  PA    NE      1    0.350000   000000

[ moleculetype ]
 ; name  nrexcl
 ABC         3

[ atoms ]
 ;   nr  type    resnr   residu  atom    cgnr    charge mass
 1  opls_997        1       ABC    PA      1        1.0000  100.0000
 2  opls_998        1       ABC    NE      1       -1.0000  100.000

[ constraints ]
  1   2   1    0.35000


pr.mdp
title               =  cpeptid position restraining
cpp                 =  /usr/bin/cpp
constraints         =  none
integrator          =  md
dt                  =  0.001    ; ps !
nsteps              =  250000      ; total 1.0 ps.
nstcomm             =  1
nstxout             =  10
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype         = PME
vdwtype             = cut-off
rcoulomb            =  1.0
rvdw                =  1.4
fourierspacing      = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order           = 4
ewald_rtol          = 1e-5
optimize_fft        = yes
constraint-algorithm     = SHAKE
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
tc-grps  =system
ref_t =   400
; Pressure coupling is not  on
Pcoupl              = no
pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  400.0
gen_seed            =  173529