Hi all,
I have never simulated membrane protein by aMD before. I fount out that
for my system there is no dihedral boost or at least this was indicated
by the amd.log file:
5000 5000 -145668.283969776472 13842.028913647868
0.847615823548 1.000000000000 103.481190357405 0.000000000000
5000 10000 -145496.101579537615 13881.695400648750
0.865654305358 1.000000000000 78.788097567655 0.000000000000
5000 15000 -145491.997313081985 13871.623936772346
0.866091288059 1.000000000000 78.237603673259 0.000000000000
I was surprised because I use dual boost.
Below you can see my input file. I use Charmm FF. For the boost
parameters calculations I used the protein + lipids number of residues,
which seems to me more logical. What might be the problem?
Thanks in advance for any ideas!
&cntrl
irest=1,
ntx=5,
imin=0,
dt=0.002,
ntc=2,
tol=0.0000001,
iwrap=1,
cut=8.0,
ntt=3,
ig=-1,
gamma_ln=2.0,
temp0=303.15,
barostat=1,
csurften=3,
ntp=3,
ntb=2,
gamma_ten=0.0,
ninterface=2,
taup=8.0,
ntpr=5000,
ntwr=5000,
ntwe=0,
ntwx=10000,
ntxo=1,
ioutfm=1,
nstlim=125000000,
iamd=3, EthreshD=13647,
alphaD=347, EthreshP=-144364,
alphaP=15135,
/
Regards,
Filip
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Received on Fri Oct 07 2016 - 20:30:03 PDT
