[gmx-users] Pullin dhiedral angle version 2016

[Luca Retattino]

Hello, I’m trying to use the pull code in my RNA system.
After a week I was finally able to make it work. But I have some problems
This is what I wanted to do:
In my system I have a bulge and I would like to se what happen to the rest of the structure if the bulge is completely outside from the double helix or if it is inside it. 

This is the map file
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_init	   = -70
pull_coord1_rate	   = -15
pull_coord1_k		   = 1000
pull-coord1-start	   = yes

The problem that I have are the following:
1) If the simulation is long and the value for K is very high, the structure breaks and the simulation stops.
I think is a problem of boundary conditions. I thought that after the angle is arrived at 180 then it would start automatically to come back…
Is this the problem? how can I solve this?

2)when I do the grompp command I noticed also something weird:
It says that all the 6 groups have been read, but after the information on the fouler grid it just print 2 groups (the first and the second) giving me these informations:
pull group	atoms	pbc atom      distance at start     	reference at t=0
1			5		 166		
2			5		 230			75.082			 5.082

Now I now the distance and the reference at t=o, but why it gives me only for the second one? why dose it pick only the middle atoms for the pbc? It should take the COM of the groups. Why it shows only the first 2 groups?

Thanks for the help

Luca