Hi Samuel,
Thanks for your help!
I don't know whether this relates only to my system, which was created
by the standard Charmm-GUI protocol, or this is more general problem.
The only more or less reasonable solution to obtain some adequate boost
is to calculate aD via 3.5*(number of residues)*0.3 (not 0.2) and then
to add 3 times aD to the cMD calculated D energy.
I will check the membrane stability. In the case of only up to 4
kcal/mol boosts there was no any significant problem.
Regards,
Filip
На 8.10.2016 г. в 15:39 ч., Samuel Bowerman написа:
> 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 - 14:00:02 PDT
