[AMBER] Problem with aMD on membrane protein and/or the amd.log file

From: filip fratev <fratev.biomed.bas.bg>
Date: Sat, 8 Oct 2016 06:02:36 +0300

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!

   iamd=3, EthreshD=13647,
   alphaD=347, EthreshP=-144364,



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Received on Fri Oct 07 2016 - 20:30:03 PDT
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