[gmx-users] Problem in pullx file

[Aswathy]

Dear Gromacs users,

I am doing SMD of a ligand pathway, and then want ot do the PMF analysis.
Initially I pulled the ligand from extra to intracellular side of the
protein. The pull code used are given below.

pull                     = umbrella
pull_geometry            = distance
pull_dim                 =  N N Y
pull_start               = yes
pull_nstxout             =  10
pull_nstfout             =  10
pull_ngroups             =  1
pull_group0              =  r_57
pull_group1              =  r_C1
pull_rate1               =  0.005
pull_k1                  =  1000

here group0 is one residue at the extracellular region and r_C1 is the side
chain Carbon atom of the ligand.

My question is , the total length of the channel is almost 40 Angstrom and
as per my knowledge, when we did the pulling the pullx file will give the
coordinate of the ligand through the channel.
Even though ligand reaches the opposite end of the channel, in pullx file I
am getting around 19 Angstrom in total.

Again I calculate the g_dist of the ligand and the center of the channel, it
shows around 40 Ang in total . Please find the links provided

Am I misunderstanding anything about the pullx file.

Could you please suggest me where thing get wrong?

http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en

http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en


Thank you,
-- 
-Aswathy
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