Dr. Simmerling,
I believe that you are correct regarding the lack of support for my system
geometry with implicit solvation. Looking in the AMBER 20 manual
(corresponding to the version of AMBER that is installed on my local
machine), I see that the main mentions of distance restraints (in the
context of *sander*) are found in the *NMR Refinement *chapter (Chapter
27). I also see mention of the *makeDIST_RST *program in this chapter,
which can take in a seven-column input (-upb) that looks something like:
23 ALA HA 52 VAL H 3.8 # comments go here (as given in the manual).
I did not see a direct interpretation of these constraints (other than HA
and H are atom types, and that 3.8 is an "upper bound" in Angstroms). Am I
correct in assuming that this performs a distance restraint between HA (on
Residue 23 named ALA) and H (on Residue 52 named VAL) with a distance of
3.8 Angstroms? There is also an 8-column format
If my understanding is correct, how can I implement this to my large system
so as to enforce the 60 mM concentration?
On Mon, Mar 21, 2022 at 12:34 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> For large systems, explicit solvent may be faster than implicit. But a
> bigger question may be about the system boundary - will your system behave
> properly if there is no periodic boundary? I don't think that there is
> support to maintain your cubic system geometry in implicit solvent unless
> you add some type of restraints. Since there is no defined volume, the
> system is infinitely dilute and will no longer correspond to 60 mM.
>
> On Mon, Mar 21, 2022, 7:28 AM Nathan Black <nathanblack262.gmail.com>
> wrote:
>
> > Hello AMBER Users,
> >
> > I am attempting to simulate a very large system (2500 anionic surfactants
> > and 2500 organic counterions, a grand total of ~150K atoms) in a (245
> > Angstrom)^3 cubic region to approximate a 60 mM surfactant solution, as
> > defined in Packmol.
> >
> > My purpose in doing this is to model aggregation behavior- as some
> > surfactant micelles related to mine are known to have aggregation numbers
> > (N) in the 300-400 range, I wanted to add a larger number of surfactants
> so
> > that (assuming some degree of adherence to experimental findings)
> multiple
> > micelles would form in each simulation.
> >
> > To reduce the computational expense of a simulation for this large
> system,
> > I attempted to set a nonbonded interaction cutoff of 10.0 Angstroms (cut
> =
> > 10.0), choose a Generalized Born implicit solvation model (igb = 5), and
> > run using GPUs (implementation with pmemd.cuda). However, I received an
> > error message when attempting this simulation- I did some further digging
> > and found that the nonbonded interaction cutoff must be set to the system
> > size when igb > 0 while using pmemd.cuda.
> >
> > I will experiment with reducing the size of the system, but are there any
> > known workarounds to this? I ask that question knowing that this design
> was
> > probably intentional.
> >
> > I understand that it is good practice to set a large cutoff when working
> > with implicit solvent, but at this point the simulations would run for
> far
> > too long to be useful, given that my system (the minimization of one such
> > 60 mM surfactant "solution" took about 24 hours when run on CPUs with
> cut =
> > 10.0) is incredibly large.
> >
> > Let me know if there is any other information I can give to help answer
> my
> > question. Any help is much appreciated.
> >
> > Thanks so much,
> > NDB
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> >
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Received on Tue Mar 22 2022 - 13:00:03 PDT
