[gmx-users] Senthil Kandasamy,about hole again

[nanyu101]

Dear Dr.Senthil Kandasamy 
  Thanks for your kind assistant.My problem is not how to minimize the bilayer+ion channel,but I can't run mdrun of my maken the hole bilayer.I did as follows.
1.Minimize my bilayer( downloaded from Dr.Tieleman's web,popc128a.pdb)The results are the follows:
Steepest Descents did not converge in 63 steps
  Potential Energy  = -1.40976e+05
Maximum force:  1.45683e+03

em.mdp
title               =  Yo
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
emstep              =  0.02	; ps !
nsteps              =  20000	; total 10 ps.
emtol               =  200
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
pme_order           =  4
fourierspacing      = 0.12
optimize_fft        = yes
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
Pcoupl              =  no
Tcoupl              =  no
gen_vel             =  no


Because it didn't converge,so I run energy minimization again.
I think I succeeded.

Steepest Descents:
   Tolerance         =  2.00000e+02
   Number of steps   =        20000

writing lowest energy coordinates.

Steepest Descents converged to 200 in 767 steps
  Potential Energy  = -1.76481e+05
Maximum force:  1.66515e+02
md.mdp
title               =  Yo
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
emstep              =  0.02	; ps !
nsteps              =  20000	; total 10 ps.
emtol               =  200
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
pme_order           =  4
fourierspacing      = 0.12
optimize_fft        = yes
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps		    =  POPC	SOL
tau_t               =  0.1	0.1
ref_t               =  300	300
; Energy monitoring
energygrps	    =  POPC	SOL
; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529


I think it's fine now and I try to make a hole in it.
make_hole.pl ....................,
And then  I run grompp .................
And then I run mdrun..................
My run.mdp and hp.mdp are following.

title               =  Yo
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.0001	; ps !
nsteps              =  20000	; total 10 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
pme_order           =  4
fourierspacing      = 0.12
optimize_fft        = yes
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
Tcoupl              =  berendsen
tc-grps		    =  POPC	  SOL
tau_t               =  0.1	  0.1
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
ref_t               =  300	  300
gen_vel             =  no


holetype                 = Cyl
hfm                      = 300
supf                     = 20
molsurf_log              = gsurf.log 
hr			 = 1.1
hx			 = 3.2
hy			 = 3.2
hz			 = 5.0
hp1 			 = 1
hp2 			 = 6654
s1 			 = 6655
s2			 = 25961
hz1 			 = 3.3
hz2 			 = 7.3
sfm 			 = 10.0 
sofs			 = 0.15 
molsurf_file             = 
debugsurf 		 = yes
resforces  		 = yes

But I failed in mdrun,the system told me as follows.
  Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.000234   1600   1601   0.000006
        After LINCS         0.000005   5546   5547   0.000001

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    1.25968e+04    8.91394e+03    1.13075e+03   -1.41875e+03    2.73782e+04
        LJ (SR)   Coulomb (SR)   Coulomb (LR) Position Rest.      Potential
   -9.55075e+03   -9.68782e+04   -7.57314e+04    1.50472e+03   -1.32055e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    4.88692e+04   -8.31854e+04    4.43307e+02    1.75477e+03

           Step           Time         Lambda      Annealing
           4780        0.47800        0.00000        1.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.000247   1600   1601   0.000006
        After LINCS         0.000006   1573   1592   0.000001

I don't know the reason.Maybe you can resolve my puzzle.Thanks for your former comments.That comments gave me many assistants.

Best wishes,
Xianhui Wu 

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