[gmx-users] Gromacs 2016 pulling code

Luca Retattino luca.retattino at ki.se
Thu Aug 3 17:30:55 CEST 2017


I´m using grimaces 2016 to pull a dihedral angle.
With the angle I can force the flipping in and out of a single bulge in a RNA system.
I tried with different k.
I do a simulation of 180 ns with a rate of 1 degree each ns. I always put the reference at 0 degree
I have obtained different results:
	Sometime when I see the file pullx.xvg it says that my COM is changing but in reality it dose not.
	When I see the trajectory with VMD I can see that the bulge is not moving.

Some other time instead (changing randomly k), the bulge moves, but it dose a rotation of 180 degrees with few steps and for the rest of the simulations stay steady.
Some other time it continues 'to be pulled’ and break the structure.

Any suggestion?

This is the part for the pulling:

pull-coord1-geometry  	   = dihedral
pull-coord1-groups	           = 1 2 3 4 5 6  
pull-group1-pbcatom 	   = 0
pull_group1_name  	   = phospate_6
pull_group2_name  	   = phospate_8 
pull_group3_name  	   = phospate_8
pull_group4_name  	   = U7 
pull_group5_name  	   = U7
pull_group6_name  	   = bulge
pull_coord1_rate	   = 1
pull_coord1_k		   = 100. (I modify this)
pull-coord1-start	   = yes
pull-coord1-init	   = -59.903

Thanks for the help!

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