[gmx-users] gmx distance

[Justin Lemkul]

On 1/31/18 11:22 AM, rose rahmani wrote:
> 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?

Your output is completely consistent. You're applying a biasing 
potential along the z-dimension only, so that's the only distance that 
mdrun cares about in establishing the reaction coordinate. The pullx.xvg 
file contains the COM coordinate of the "reference" group (group0) and 
in your case is just the z-coordinate, so that's the first data column. 
The second data column (dZ) is the displacement along the z-axis. Your 
COM distance results confirm this - your protein and ZnS are not exactly 
coincident; they have different x and y coordinates. But the z column in 
the distance output agrees with the pullx.xvg file (when considering the 
absolute value).

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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