[gmx-users] Re: Adsorption layer of water molecules

[ypca]

Actually, I used trjconv (nojump) and these are the images of the run after
the post-processing. 
I didn't understand very well what you mean with the box vectors of the
starting and ending.
When I used editconf, it has shown:

box vectors :  7.205 10.465 11.742 (nm) 
new box vectors :  7.589  7.589  7.589 (nm) 

The .mdp files I have used:

NVT

title                    = 1ns_pr_fixo
cpp                      = /lib/cpp
define                   = -DPOSRES
integrator               = md
tinit                    = 0
dt                       = 0.002
nsteps                   = 500000 ; total 1000 ps
comm-mode                = Linear
nstcomm                  = 1
nstxout                  = 100
nstvout                  = 100
nstfout                  = 100
nstlog                   = 100
nstenergy                = 100
nstxtcout                = 100
xtc-precision            = 1000
constraint_algorithm     = lincs
lincs_iter	         = 1		
lincs_order	         = 4		
energygrps               = Protein Non-Protein 	
nstlist                  = 5
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0
domain-decomposition     = no
coulombtype              = PME
pme_order                = 4
fourierspacing           = 0.16
rcoulomb                 = 1.0
vdw-type                 = Cut-off
rvdw                     = 1.0
DispCorr                 = EnerPres
optimize_fft             = yes
Tcoupl                   = V-rescale
tc-grps                  = Protein Non-Protein 
tau-t                    = 0.1        0.1
ref-t                    = 348        348
gen_vel                  = yes
gen_temp                 = 348
gen_seed                 = -1
Pcoupl                   = no
compressibility          = 4.56e-5
constraints              = all-bonds
unconstrained-start      = no
morse                    = no

NPT

title                    = 1000ps_pr_fixo
cpp                      = /lib/cpp
define                   = -DPOSRES
integrator               = md
tinit                    = 0
dt                       = 0.002
nsteps                   = 500000 ; total 1000 ps
comm_mode                = Linear
nstcomm                  = 1
nstxout                  = 100
nstvout                  = 100
nstfout                  = 100
nstlog                   = 100
nstenergy                = 100
nstxtcout                = 100
xtc-precision            = 1000
energygrps               = Protein Non-Protein 	
constraint_algorithm     = lincs
lincs_iter	         = 1		
lincs_order	         = 4		
nstlist                  = 5
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0
domain-decomposition     = no
coulombtype              = PME
pme_order	         = 4
fourierspacing	         = 0.16
rcoulomb                 = 1.0
vdw-type                 = Cut-off
rvdw                     = 1.0
DispCorr                 = EnerPres
optimize_fft             = yes
Tcoupl                   = V-rescale
tc-grps                  = Protein Non-Protein 
tau-t                    = 0.1        0.1
ref-t                    = 348        348
gen_vel                  = no
gen_temp                 = 348
gen_seed                 = -1
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = Isotropic
tau_p                    = 1.0
compressibility          = 4.56e-5
ref_p                    = 1.0
refcoord_scaling         = com
constraints              = all-bonds	
unconstrained-start      = no
morse                    = no

PRODUCTION

title                    = 100 ns
cpp                      = /lib/cpp
include                  = 
define                   = 
integrator               = md
tinit                    = 0 
dt                       = 0.002
nsteps                   = 50000000 ;100ns 
comm-mode                = Linear
nstcomm                  = 1
nstxout                  = 50000 ; trr
nstvout                  = 50000 ; velocidades
nstfout                  = 50000 ; forcas
nstlog                   = 1000
nstenergy                = 1000
nstxtcout                = 10000 ; xtc
xtc-precision            = 1000
constraint_algorithm     = lincs
lincs_iter	         = 1		
lincs_order	         = 4	
energygrps               = Protein Non-Protein       
nstlist                  = 5
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0
domain-decomposition     = no
coulombtype              = PME
pme_order	         = 4
fourierspacing	         = 0.16		
rcoulomb                 = 1.0
epsilon-r                = 1
vdw-type                 = Cut-off
rvdw                     = 1.0
DispCorr                 = EnerPres
optimize_fft             = yes
Tcoupl                   = V-rescale
tc-grps                  = Protein Non-Protein     
tau-t                    = 0.1        0.1   
ref-t                    = 348        348 
gen_vel                  = no
gen_temp                 = 348
gen_seed                 = -1
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = Isotropic
tau-p                    = 2.0
compressibility          = 4.56e-5
ref-p                    = 1.0
constraints              = all-bonds
unconstrained-start      = no
morse                    = no


Thanks a lot 



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