[gmx-users] about make_hole's error

[nanyu101]

Dear gmx-users,

  Now,I think I have succeeded in minimizing the lipid,but I still can't make a hole in bilayer.I will show you the error after my energy minimization.The first part of my following message is my results of energy minimization.The second part of my following message is my parameters and results of md_make_hole.

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


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


The message about md_make.hole.

starting mdrun 'popc'
20000 steps,      4.0 ps.

step 2880, will finish at Fri Feb 21 19:04:49 2003
Step 2885, time 0.577 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.174774 (between atoms 3447 and 3448) rms 0.003554
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
...............................

..................................

Step 3001, time 0.6002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 241.992508 (between atoms 3436 and 3437) rms 5.756467
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3433   3436  178.5    1.7229  33.3260      0.1470
   3434   3436  179.1    1.7235  33.3271      0.1470
   3435   3436  178.3    1.6982  33.3284      0.1470
   3436   3437  177.6    1.7317  35.7199      0.1470
   3437   3438  160.4    0.3393  10.6832      0.1530
   3438   3439   96.3    0.1571   2.0529      0.1430
   3439   3440   41.0    0.1592   0.1950      0.1610

Step 3002, time 0.6004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 2926611881093234688.000000 (between atoms 3436 and 3437) rms 68641282561409024.000000
bonds that rotated more than 30 degrees:
.................................

   3642   3644   86.9    0.1470   0.4678      0.1470
   3643   3644   89.6    0.1470   3.3229      0.1470
   3644   3645   88.4    0.1470   1.0649      0.1470
   3645   3646   89.3    0.1530   1.1499      0.1530
   3646   3647   89.2    0.1430   0.5002      0.1430
   3647   3648   38.5    0.1610   0.1997      0.1610
Wrote pdb files with previous and current coordinates




The run.mdp and hp.mdp list as follows.



run.mdp

title               =  Yo
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002 ; 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




hp.mdp



holetype                 = Cyl
hfm                      = 10
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








Best wishes,

Xianhui WU

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