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

[Justin Lemkul]

On 2/8/13 12:11 PM, ypca wrote:
> Actually, I used trjconv (nojump) and these are the images of the run after
> the post-processing.

Then the output is exactly what you should be seeing.  If you remove jumps, then 
molecules simply diffuse outward.  There is nothing wrong at all with the 
trajectory.

> 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)
>

I wanted to see this to make sure the box wasn't doing anything funny.  As you 
can see, there are indeed some changes in the box, but it got smaller over time, 
not vastly larger if the water molecules were actually diffusing out into the void.

Conclusion: nothing wrong.  For proper visualization, trjconv -pbc mol -ur 
compact with or without -center if you want to center the protein.

-Justin

> 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
>
>
>
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/Adsorption-layer-of-water-molecules-tp5005243p5005354.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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