[gmx-users] problem regarding pr.mdp file of protein embedded in popc

[sudheer babu]

Dear gmx-users,
I have inserted my protein into membrane. I did energy minimisation with
Steepest descent, that output used for input of position restrain, this "EM
out.gro" structure is fine . When I do Position restrain, this step  goes
fine  but,  popc structure of " PR out.gro " looks tilted.  Where is the
error happening?
I am mentioning my pr.mdp file
Pls help me.  Thanks in advance

title                 =   Protein in popc restrained
define              =  -DPOSRES
constraints       =  all-bonds
integrator         =  md
dt                    =  0.002    ; ps !
nsteps             =  10000    ; total 50 ps.
nstcomm          =  1
nstxout             =  50
nstvout             = 1000
nstlog               =  10
nstenergy         =  10
nstlist              =  10
ns_type            =  grid
rlist                  =  0.9
coulombtype     =  PME
rcoulomb          =  0.9
rvdw                =  1.4
pbc                 =  xyz
; Berendsen temperature coupling is on in two groups
Tcoupl             =  Berendsen
tc-grps            =  POPC   Protein   SOL_Cl
tau_t               =  0.1     0.1      0.1
ref_t                =  310     310      310
; Anisotropic pressure coupling is now on
Pcoupl               =  berendsen
pcoupltype         =  anisotropic
tau_p                 =  1.0      1.0     1.0     1.0     1.0     1.0
compressibility    =  4.5e-5   4.5e-5  4.5e-5  0       0       0
ref_p                  =  1.0      1.0     1.0     1.0     1.0     1.0
; Energy monitoring
energygrps          =  POPC  Protein  SOL_Cl
; Generate velocites is off at 300 K.
gen_vel              =  yes
gen_temp           =  310
gen_seed           =  173529
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