Dear Amber users !
I would like to train myself a bit in the application of the protocols
using pulling algorithms to move some selection of the atoms during the
simulation. E.g. what I have already seen from the available tutorials:
https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial
For my case-study I am dealing with the modeling of a transmembrane peptide
embedded into the membrane system, using packmol-memgen and would like to
(so probably to pull along "Z") to remove it from the membrane into the
water.
Assuming that the tutorial looks for me a bit complex ( I am a master
student in biotechnology) could you please advise me some introductory
steps for such a setup, e.g. what should I add directly to my md.in file to
introduce such pulling force with given direction, force and time ?
Here is my md.in file (without any pulling):
pro 10ns at 303K
&cntrl
imin=0, ntx=5, irest=1,
ntc=2, ntf=2, tol=0.0000001,
nstlim=5000000, ntt=3, gamma_ln=1.0,
temp0=303.0,
ntpr=5000, ntwr=500000, ntwx=5000,
dt=0.002, ig=-1,
ntb=2, cut=10.0, ioutfm=1, ntxo=2,
ntp=3, csurften=3, gamma_ten=0.0, ninterface=2,
/
Many thanks in advance !
Enrico
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Received on Wed Apr 10 2024 - 01:00:02 PDT
