Dear Jason,
>> I use PME & would like to continue to use PME.
>> Resurrecting an old copy of sander? uff...
>
> I would actually suggest that you really _don't_ want to use PME for
> this particular calculation. What you're effectively trying to do is
> eliminate the intra-molecular nonbonded interactions so that you can
> compute the inter-molecular nonbonded interactions exclusively. It
> seems that the strategy is to compute the full electrostatics (using
> PME) and then subtract out the intramolecular nonbonded energies (using
> no PME and a group-based cutoff of 0 to ensure that atoms interact only
> with other atoms in the same residue).
>
> This is a trick that takes advantage of a key assumption: each solvent
> molecule is made up of a single residue only.
Yes
>> Does it means this is not possible to carefully study/check solvent
>> boxes with Amber nowadays?
>
> I've never tried pure group-based cutoffs with no Ewald sum. It may not
> work anymore since it's a somewhat unusual simulation (nor is it
> particularly general since it relies on the above assumption). If
> group-based cutoffs still work and the assumption above holds for your
> system, that's the easiest solution. There are alternatives, though,
> that depend on the nature of your 'molecule'.
>
> 1) Does the molecule have any atoms that are no farther than 2 bonds
> away? If not (like with water and chloromethane), then there are no
> intramolecular nonbonded interactions and this step is unnecessary.
>
> 2) Does the molecule have any atoms that are no farther than 3 bonds
> away? If not (like with ethane and ethanol), then you can simply ignore
> the 1-4 VDW and 1-4 EEL contributions (again, making this step
> unnecessary).
These two cases are more simple - Yes, we can reproduce dHvap for
small model cases.
> 3) The most tedious scenario if there are intramolecular energies you
> need to get rid of. You can, using ParmEd, zero out the charges and van
> der Waals parameters for every molecule *except* the molecule whose
> intramolecular NB interactions you want and simply compute a
> (non-periodic) energy in which you know the EEL and VDW contributions
> are strictly intramolecular. You can then do this for every molecule in
> your system and sum them up to get the total intramolecular nonbonded
> energy (or, alternatively, if your molecules are rigid due to
> constraints you can simply multiply by the number of molecules you
> have).
You are right - this is the case we are interested in;
examples: DMSO or cyclohexane.
> If you are comfortable with Python programming, you can do step 3 in a
> single Python script using the ParmEd API like so:
>
> from chemistry.amber.readparm import AmberParm
> from ParmedTools.ParmedActions import change, addljtype
>
> for i in range(num_molecules):
> parm = AmberParm('path/to/prmtop')
> change(parm, 'CHARGE', '!:%d' % i, 0.0)
> addljtype(parm, '!:%d' % i, radius=0.0, epsilon=0.0)
> parm.writeParm('tmp.parm7')
> # System call to compute energy
I got your point: the problem is that vdW param. are not repeated for
each molecule of a solvent box in the prmtop as the charge values are;
Anyway, we will try to do something ;-)
Yes your detailed explanations help a lot,
thank you very much,
regards, Francois
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Received on Tue Feb 25 2014 - 23:00:02 PST
