[gmx-users] Pull code - 2

[DimitryASuplatov]

Hello,

I was running different simulations with the following pull code

1/ 
;-----------PULL CODE ---------------------

pull    =       umbrella
pull_geometry   = direction
pull_group1     = r_535
pull_vec1       = 0.51 0.026 0.273
pull_k1         = 110
pull_rate1      = 0.002 ; nm/ps = 20 A/ns
pull_start      = yes
pull_init1      = 0

2/ Different pull group

;-----------PULL CODE ---------------------

pull    =       umbrella
pull_geometry   = direction
pull_group1     = r_538
pull_vec1       = 0.51 0.026 0.273
pull_k1         = 110
pull_rate1      = 0.002 ; nm/ps = 20 A/ns
pull_start      = yes
pull_init1      = 0


3/ Two pull groups

;-----------PULL CODE ---------------------

pull    =       umbrella
pull_geometry   = direction

pull_ngroups    = 2

pull_group1     = r_533
pull_vec1       = 0.51 0.026 0.273
pull_k1         = 110
pull_rate1      = 0.002 ; nm/ps = 10 A/ns
pull_init1      = 0

pull_group2     = r_538
pull_vec2       = 0.51 0.026 0.273
pull_k2         = 110
pull_rate2      = 0.002 ; nm/ps = 20 A/ns
pull_init2      = 0

pull_start      = yes


Additionaly I`ve added the following lines to each file
comm-mode           = angular
nstcomm             =  10


I have constructed the pull vector by taking the coordinates of CA of
pull_group and coordinates of OW in a water molecule that was
positioned in the direction I wanted to pull. Finally, I have calculated the
vector by substraction (x2(water) - x1(CA_aminoacid); y2-y1; z2-z1). 

Observing the results of my simulation I have observed two problems:

1/ Groups are pulled not exactly in the same direction differing by about 45 degrees. I guess that means that system is rotating even though I set comm-mode to angular!!!
2/ The first 5 ns I see no indication of pulling and the force is climbing evenly. Then I see a huge force leap up followed by a leap down (in some picoseconds) corresponding to displacement of pull group.
I just don`t understand why force is growing so fast. 

What am I doing wrong? Any suggestions?
Thank you. I appreciate your time.

SDA