[gmx-users] mdrun_hole problem again

[chris.neale at utoronto.ca]

- you didn't do an energy minimization
- you used hz1 0 and I used hz1 1.0
- you didn't include make hole options hr,hx,hy

*** Somebody already suggested nstlog = 1 and nstenergy = 1, please try that!!!
In fact make everything 1 (nstxout,nstxtcout,...)

Here is what worked for me with the same POPE file:

1. Do an energy minimization

2. run the make_hole mdrun:

grompp -maxwarn 10000 -f grompp_md.mdp -c a.gro -p a.top -o a.tpr

mdrun -nice 4 -hole -holep hole.mdp -s a.tpr -o a.trr -c b.gro -g output.mdrun
-v -x a.xtc 

############################# em.mdp ############################

title               =  energyMinimization
cpp                 =  /usr/bin/cpp
integrator          =  steep
nsteps              =  500
emtol               =  200
emstep              =  0.000005
comm_mode           =  linear
nstcomm             =  1
comm_grps           =  System
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  PME
fourierspacing      =  0.15
pme_order           =  4
vdwtype             =  switch
rvdw_switch         =  0.9
rvdw                =  1.0
rlist               =  1.1
DispCorr            =  no
Pcoupl              =  no
tcoupl              =  no
annealing           =  no
gen_seed            =  9896
constraints         =  hbonds
constraint_algorithm=  shake
shake_tol           =  0.0001


############################# hole.mdp ############################

holetype                 = Grasp_ascii
hfm                      = 10
supf                     = 10
molsurf_log              = make_hole.log
hr                       = 0
hx                       = 0
hy                       = 0
hz                       = 3.5
hp1                      = 1
hp2                      = 17680
s1                       = 17681
s2                       = 43934
hz1                      = 1.0
hz2                      = 6.0
sfm                      = 10.0
sofs                     = 0
molsurf_file             = pagpsys_tot_e.surf
debugsurf                = no
resforces                = yes

############################ run.mdp #################################
title               =  seriousMD
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
integrator          =  md
nsteps              =  10000
tinit               =  0
dt                  =  0.002
comm_mode           =  None
nstcomm             =  1
comm_grps           =  System
nstxout             =  10000
nstvout             =  10000
nstfout             =  10000
nstlog              =  100
nstlist             =  10
nstenergy           =  10000
nstxtcout           =  250
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  Cut-off
;fourierspacing      =  0.15
;pme_order           =  4
vdwtype             =  switch
rvdw_switch         =  0.9
rvdw                =  1.1
rlist               =  1.1
rcoulomb            =  1.1
DispCorr            =  no
Pcoupl              =  Berendsen
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.
tcoupl              =  nose-hoover
tc_grps             =  POPE SOL
tau_t               =  0.05 0.05
ref_t               =  300. 300.
annealing           =  no
gen_vel             =  yes
gen_temp            =  300.
gen_seed            =  9896
constraints         =  hbonds
constraint_algorithm=  shake
shake_tol           =  0.0001