Dear Amber Users,
I want to perform a simulation in which I want to set a fixed distance
between atoms of two different residues.
I have generated 10 unfolded states of a protein and for all of them I want
to make the distance between C-Alpha atom (residue 2) and N atom(residue
64) to be 2.5 while running an MD (initial distances are different in all
10 cases). For example, if the distance between C-Alpha atom (residue 2)
and N atom(residue 64) is 10.6, during simulation I want to decrease the
distance from 10.6 to 2.5 and then remove the restrains. In Amber 12
reference manual (p-230) something like this is mentioned with center of
mass but I could not fix it for my case. I would appreciate any help in
order to perform such simulations by modifying the md.in file which I have
as follows:
md.in file:
DNA 14mer
&cntrl
imin = 0, irest = 1,
ntx = 7, ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0
nstlim = 5000000, dt = 0.002,
ntpr = 10000, ntwx = 10000, ntwr = 10000
/
Regards,
Jac
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Received on Sat Nov 04 2017 - 07:00:02 PDT
