[gmx-users] problem about Pr.mdp

[sudheer babu]

Thanks Mr.Mark for your reply,
I am not getting any error, but after Position restrain step, when I see the
structure of *pr_protein_popc_out.gro in VMD the POPC tails are tilting
towards backwards(like pulling). It looks there is gap inbetween two
membrane layers, middle part of the protein appears without covering POPC
moledules, but water and protein structure are fine.
Can you pls tell where is the problem ? Is there in any mistake in my *
pr.mdp file
I am gving description about what steps i have done:
1.The protein simulated in solution for 500ps .
2. Protein inserted into POPC by using "genbox".
3. Steepest gradient energy minimisation for "protein embedded in POPC
system"  , here strucure is fine
4. Postion restrain for same system
 - For Protein, POPC and Water force constant -10000 I have used.

I am mentioning my *pr.mdp file
title               =   popc restrained
define              =  -DPOSRES  -DPOSRES_LIPID  -DPOSRES_WATER
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  10000    ; total 50 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
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 on at 300 K.
gen_vel             =  yes
gen_temp            =  310
gen_seed            =  173529

Thanks in advance.
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