Hi Filip,
The threshold energy defined by aMD (EthreshD) sets the cut-off for
potentials that require boosting. If your energy is above this threshold,
then that component of the energy won't be boosted. Taking a look at your
amd.log, your printed dihedral energies are all roughly 13850 kcal/mol, but
your threshold is 13647. Raising EtheshD should boost your dihedrals, but
I can't say for certain what that will do to the stability of your
membranes, as I have also never run aMD on a memberane before.
Take care,
Samuel Bowerman
Ph.D. Candidate
Department of Physics
Illinois Institute of Technology
On Fri, Oct 7, 2016 at 10:02 PM, filip fratev <fratev.biomed.bas.bg> wrote:
> 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 Sat Oct 08 2016 - 06:00:04 PDT
