[gmx-users] Reg. Umbrella sampling problem with direction

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Hello Everyone,


I am novice in umbrella sampling. I did followed Dr. Justin's tutorial and it works fine for me. However, I would like to transport solute (along z-axis) from an ion channel (intracellular to extracellular site) so I made the system (Protein+solute+DPPC+Sol+ion) and came upto the Step 5 of tutorial successfully. Now I wanted to get the distances among frames using perl distance.pl but I just get the frame number. So, I seek your advice and suggestion on the input parameter of Pull-code.

Here is the pull-code I used for the simulation. 

; Pull code
pull                                 = yes
pull_ngroups                  = 2
pull_ncoords                  = 1
pull_group1_name        = Protein
pull_group2_name        = DRG
pull_coord1_type          = umbrella      ; harmonic biasing force
pull_coord1_geometry  = direction    
pull_coord1_groups      = 1 2
pull_coord1_dim           = N N Y
pull_coord1_vec            = 0 0 1
pull_coord1_rate            = 0.01          ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k                = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start           = yes           ; define initial COM distance > 0


Please guide in making correct input parameter for pull-code 

I get this output in pullx.xvg file

@    title "Pull COM"
@    xaxis  label "Time (ps)"
@    yaxis  label "Position (nm)"
@TYPE xy
0.0000 -2.51551
0.1000 -2.50136
0.2000 -2.49201
0.3000 -2.49526
0.4000 -2.47566
0.5000 -2.4618
0.6000 -2.47792
0.7000 -2.47152
0.8000 -2.48659
0.9000 -2.49259
1.0000 -2.53279
1.1000 -2.53133
1.2000 -2.51926
1.3000 -2.51488
Or how can I use this output to calculate the distance among the frames and further use for g_wham program.




Looking forward to interact with you.
Regards,


Changdev