[gmx-users] gmx distance

[rose rahmani]

Hi,
This is md_pull.mdp

integrator               = md
dt                       = 0.001
nsteps                   = 4000000
nstxout                  = 1000
nstvout                  = 1000
nstfout                  = 500
nstlog                   = 500
nstenergy                = 500
nstxtcout                = 500
nstlist                  = 10
rlist                    = 1.5
coulombtype              = pme
rcoulomb                 = 1.5
vdwtype                  = Switch
rvdw_switch              = 1.0
rvdw                     = 1.2
pcoupl                   = no
gen_vel                  = no
constraints              = h-bonds
ns_type                  = grid
pbc                      = xy
freezegrps               = WAL ZnS
freezedim                = Y Y Y Y Y Y
energygrp-excl           = WAL WAL ZnS ZnS
energygrps               = SOL WAL ZnS Protein NA CL
nwall                    = 2
wall-atomtype            = C C
wall-type                = 9-3
wall-density             = 150 150
wall-ewald-zfac          = 3
ewald-geometry           = 3dc
fourierspacing           = 0.12
tcoupl                   = v-rescale
tc-grps                  = System
tau-t                    = 0.1
ref-t                    = 300

; Pull code
pull                    = umbrella
pull_ngroups            = 1
pull_group0             = ZnS
pull_group1             = Protein
pull_geometry           = distance
pull_dim                = N N Y
pull_rate1              = -0.01
pull_k1                 = 5000
pull_start              = yes
pull_nstxout            = 50
-------------------------------------------
pullx.xvg;

@    title "Pull COM"
@    xaxis  label "Time (ps)"
@    yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.0000  4.287   1.76284
0.0500  4.287   1.75329
0.1000  4.287   1.74622
0.1500  4.287   1.73983
0.2000  4.287   1.73664
0.2500  4.287   1.7377
.
.

3999.7500       4.287   0.258632
3999.8000       4.287   0.258738
3999.8500       4.287   0.258955
3999.9000       4.287   0.260093
3999.9500       4.287   0.25843
4000.0000       4.287   0.258025
-------------------------
Then >>trjconv -f traj.xtc -s pull.tpr -n index.ndx -o confwhole.gro -pbc
whole
Then >>g_dist  -f confwhole.gro -n index.ndx -s pull.tpr -o distwhole.xvg

this is distwhole.xvg
   0.0000000    1.7630774    0.0185155   -0.0197599   -1.7628694
   0.5000000    1.7529889   -0.0133090    0.0135729   -1.7528858
   1.0000000    1.7453604   -0.0344692    0.0751038   -1.7434030
   1.5000000    1.7691813   -0.0621567    0.0087628   -1.7680674
.
.
3997.5000000    1.6120006    0.9964043   -1.2400901   -0.2605782
3998.0000000    1.6122891    0.9971979   -1.2404475   -0.2576084
3998.5000000    1.6124574    0.9966092   -1.2406733   -0.2598433
3999.0000000    1.6115565    0.9968075   -1.2396555   -0.2583475
3999.5000000    1.6120616    0.9964568   -1.2404943   -0.2588253
4000.0000000    1.6116294    0.9952377   -1.2410750   -0.2580390

as you see max dist=1.76 and min dist=1.611, but in VMD i can see that two
group (Protein and ZnS sheet) in last frame are too close to each other. so
why i see 1.611 in distwhole.xvg?

and could you please tell me what is the relevance of pullx.xvg to g_dist
output?as you see pullx.xvg ensure that distance between 2 group is
decreasing, so...?

is there anything i did not consider?

Thank you so much