Note - residue based cutoffs have NOT been supported in Sander since v6.0
(or ever in pmemd). Thus if you want to look at purely intermolecular
non-bonded interactions by relying on residue based cutoffs then you will
need to go back to AMBER 5.0 (or sander.classic from AMBER 6).
All the best
Ross
On 2/24/14, 5:45 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
>On Mon, 2014-02-24 at 10:31 +0100, FyD wrote:
>> Dear Robert,
>>
>> > The cutoff value of "0.d0" in pmemd for a pme run is equivalent to
>> > requesting that the default values be used - probably 8.0 angstrom,
>> > if memory serves, assuming igb 0 for a pme simulation.
>>
>> Yes - this corresponds to what I get...
>>
>> I compare MD simulations (with PME) with cut = 12 vs cut = 0
>> the obtained results are very similar.
>>
>> This means 'cut = O' does not do what I want; I wonder if crashing is
>> not better than generating data in this case...
>>
>> > PME does strange things at small-ish cutoff, but does not allow 0
>> > (in the sense that it says "oh, you wanted 8"), and I presume later
>> > catches and disallows cut < 0. In my experience, reducing the
>> > direct space cut below roughly 7.0 angstrom causes unacceptable
>> > error limits unless you increase grid density for reciprocal space
>> > (there is basically a balancing act between reciprocal and direct
>> > space in terms of what is necessary to keep error acceptable). And
>> > if you think long cutoffs are expensive, play around a bit with
>> > greatly increasing nfft1,2,3 in a large system :-}. So all I am
>> > really answering here is why pmemd ran - it basically ignored you...
>>
>> ok
>>
>> > I would have to read the paper done with amber 4.1 to have a clue
>> > what they were really up to,
>>
>> See http://pubs.acs.org/doi/full/10.1021/jp9717655 - It is written:
>>
>> "The heat of vaporization is computed from the average intermolecular
>> interaction energy Eint via dHvap = -Eint + RT
>> For molecules that do not have an internal nonbonded interaction
>> beyond 1?4 (e.g., the chloromethanes), Eint is calculated
>> straightforwardly as the sum of EELEC and ENONB in the SANDER output,
>> divided by the number of molecules in the system. For all other
>> molecules, EELEC and ENONB also contain contributions from
>> intramolecular nonbonded interactions. To correct for these, we
>> performed a short simulation with the nonbonded cutoff radius set to
>> zero. Due to the residue-based cutoff in AMBER, EELEC and ENONB now
>> accumulate only the intraresidue nonbonded interactions that can be
>> subtracted from the total to yield the intermolecular portion needed
>> for the calculation of dHvap."
>>
>> > but pmemd is designed to always use either
>> > pme or generalized Born, so resurrecting an old copy of sander may
>> > be your best bet..
>>
>> 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.
>
>> 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).
>
>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).
>
>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
>
>Alternatively you can write a quick NAB program to do something
>equivalent. In both cases, help can be found in the AmberTools manual.
>
>HTH,
>Jason
>
>--
>Jason M. Swails
>BioMaPS,
>Rutgers University
>Postdoctoral Researcher
>
>
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Received on Mon Feb 24 2014 - 10:00:03 PST
