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
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