[gmx-users] pull code

arnab mukherjee arinipa at gmail.com
Fri Oct 14 14:49:06 CEST 2005

dear users,

I have to seek your help regarding the umbrella sampling using pull code. I
have checked about the thing and no answer came to my notice ( i'm sorry if
I missed by chance).

The question is I pull a group from another in order to calculate the free
energy with respect to distance between the two. the input pull.ppa is given

intially i use editconf to align my
verbose = yes
runtype = umbrella
group_1 = tbr
reference_group = protein
reftype = com
Skip steps = 10
pulldim = N N Y
constraint_direction = 0.0 0.0 1.0
constraint_distance1 = 1.0
k1 = l500 ;kj/mol
pos1 = 0.0 0.0 1.0

intially i use editconf to align my group_1 along Z coordinate. i know i
have to do it before putting waters. but after minimization, the direction
changes again. now i cannot aling them again along a particular space fixed
X, Y or Z coordinate.

what to do?

2nd problem is that, if anyhow i manage to start the simulation by aligning
group_1 along any of X, Y or Z direction, after some time, both the
reference_group and the group_1 will start to tuble and thus again the
direction of alignment will change.

to overcome the situation either i can use constraint to constrain the
distance between group_1 and ref_group,

but how to do that within umbrella sampling method?

my third question is bit silly. how to modify the dynamic option within pull
code which is not working ?

thanking you all,
Arnab Mukherjee
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