Hi Charles,
I replaced the protocol.initNBond() by the xplor command and added the
ELEC potential. It did accelerate greatly the calculation, so that's one good
point. The energy for the ELEC potential is 0.00, but I guess it is normal
since I do not have actual charges in the structure. Unfortunately the
temperature variations are still of the same amplitude, maybe even bigger. I
will run longer MDs to check that.
Thanks again for the tip,
Best regards,
Olivier Serve
Le 29 juil. 2010 ? 04:50, Charles at Schwieters.org a ?crit :
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> Hello Olivier--
>
>> I have noticed that during a TAD (using IVM) at 303 K, the
>> temperature variations were around +/- 30 K. I am currently
>> working on a di-ubiquitin system with amber force field (no
>> experimental constraints, backbone fixed), >20000 steps, 50
>> ps. If I use only one monomer, the variations are almost the
>> same and if I switch this system to standard xplor forcefield,
>> the variations are more like +/- 10 K. I have few experience
>> with MD, are those variations reasonable or should I correct
>> something ?
>
> one thing to be careful of is that protocol.initNBond() should not be
> used if you're including VDW + electrostatics. Instead, you should have
> something like:
> xplor.command("""
> parameter
> nbonds
> nbxmod=5 atom cdiel shift
> cutnb=9.5 ctofnb=8.5 ctonnb=6.5 eps=1.0 e14fac=0.4 inhibit 0.25
> wmin=0.5
> tolerance 0.5
> end
> end""")
>
> and XplorPot('VDW') and XplorPot('ELEC') should be included in the
> potList.
>
>
>> I am also trying to use implicit solvent with Generalized Born
>> (hence the amber forcefield). Though I was expecting a longer
>> computing time, I have something like a 100 folds increase. It
>> seems a lot to me, from the GB test files, I was expecting
>> something like a 5 fold increase. Anyone with feedback on that
>> point ?
>
> please see what the difference is when vdw+electrostatics are properly
> included.
>
> best regards--
> Charles
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