[gmx-users] pull code question

Marino Convertino convertino at farmchim.uniba.it
Thu Mar 16 18:53:20 CET 2006

 Dear GMX users,
I am simulating the hydrophobic interaction between two 42-aminoacid oligopeptides in pbc conditions with acqueous explicit solvent with all-bonds constraints (LINCS). 
In order to allow them to interact -for the first time- I am using pull code.

My pull.ppa is as follows

verbose = no
runtype = afm
group_1 = protein_2
reference_group = protein_1
reftype = com_t0
reflag = 1
pulldim = Y Y Y

Supposing that in my sistem the two proteins (interacting groups) are distant 50 nm at time 0 and I would like to cover this distance in about 2000 ps.
Should I use an

afm_rate1 = 0.025  (50ns/2000ps)?

Can anyone suggest me the force constant value to simulate the hydrophobic interaction (afm_k1) ?
How can I set  the unit vector describing the direction of pulling (afm_dir1) ?

May I set the initial position relative to the reference group as

afm_init1 = 0 0 0

I am using GROMACS 3.2.1, does pull code work in parallel?

Sorry for the long message and I hope someone would help me.
Thanks in advance.


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