[gmx-users] Reg. Umbrella sampling problem with direction
"가디 장데부 고라크스나트"
f07338 at kist.re.kr
Tue Aug 1 03:01:39 CEST 2017
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)"
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.
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