[gmx-users] rapid change in angles of simulation cell - regd

[ramesh cheerla]

Dear Gromacs users,


                                     I am performing simulations
(crystalline)  of  a polymer crystal in Gromacs,  for these
simulations I have generated a triclinic box with angles alpha=90,
beta=125.4 and gamma=90 degrees by using editconf,  while doing  so it
has given the  warning   "WARNING: Triclinic box is too skewed".  with
generation of the output.
 In the next step I  have done energy minimization with this skewed
box, by doing so what I have observed is that,  in first step of
minimization itself beta value  is changing from 125.4 to 102 degrees.
 What might be the reason for this large change ?  and How can I fix this ?
 The .mdp file that I have used for minimization is as follows:

integrator    = steep
emtol         = 1
emstep        = 0.001
nsteps        = 1000
nstxout       = 100
nstvout       = 100
nstfout       = 100
nstlog        = 100
nstxtcout     = 100
nstlist       =  10
ns_type       = grid
pbc           = xyz
pbc           = no
rlist         = 1.0
rlistlong     =  -1
;coulombtype   =   PME
rcoulomb_switch = 0.9
rcoulomb        = 1.0
vdwtype         = cutoff
rvdw            = 1.0
rvdw_switch     = 0.9
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 6
ewald_rtol      = 1e-06
ewald_geometry  = 3d
optimize_fft    = no
morse                = no

Thank you in advance.



Regards,
Ramesh.