[gmx-users] FEP softcore problematics
mgoette at mpi-bpc.mpg.de
Wed Jun 21 14:55:34 CEST 2006
Thank you for the detailed answer.
It sounds reasonable. :)
For sure it's the best way to make the calculations separatly and sum up
the energies at the end. You mentioned, that, in the case of splitting,
the "density" of snapshot samplings at lambda=0,1 can be lower.
So I guess, one reaches approx. 30-35 samplings, when splitting the
terms. In the first place, this is no big deal, because of the
possibility of parallelization, but for screening purposes in the
future, the amount of simulation time in total is quite critical for me.
I tried to find that paper, but unfortunately didn't.
It would be great, if you could give me some more info about it, cause I
would like to have a look into it, at least.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
David Mobley wrote:
> You may be having the infamous "charge overlap" problem. In
> particular, one additional reason not to change LJ interactions at the
> same time as electrostatics is if you are inserting or disappearing
> Assume, for a moment, that you are disappearing a couple of atoms. The
> soft core for LJ allows these disappearing atoms to begin overlapping
> with other atoms before they are completely disappeared -- while they
> also have some charge. Imagine, for example, you are disappearing an
> oxygen with a negative charge. Now you find yourself in the position
> of having a negatively charged site that can occasionally overlap with
> positively charged atoms which you are NOT disappearing (especially
> things like hydrogens on water molecules, since they have 0 LJ
> parameters in most FF, but also possibly other atoms). Obviously,
> putting a positive charge extremely close to a negative charge results
> in huge forces. When this happens, the simulation will often explode
> (which, in GROMACS, usually means LINCS errors).
> This is really an additional reason to do the calculation in several
> steps, in my opinion.
> If you are desperate not to do it in two steps, there was a recent
> paper (2006, I think) from a group in England that presented an
> alternative method for handling the charge transformation that was
> designed to smooth out the singularity encountered when two opposite
> charges get really close to one another. The title had something to do
> with "charged species". The idea was to allow both the electrostatic
> and LJ transformations to be done at once, like you're trying to do.
> If you can't find the reference and want it, let me know and I will
> dig it up. I had thought at one point about implementing this into
> GROMACS, but decided it wasn't worthwhile for me since the hard part
> is the LJ transformation, anyway, and that's where I spend most of my
> CPU time, so this would be a fairly minimal savings.
> On 6/21/06, Maik Goette <mgoette at mpi-bpc.mpg.de> wrote:
>> Hi all
>> Because the fact of handling vdw and electrostatics with the same values
>> was discussed before, I won't go into much detail about what Berk and
>> David M. wrote.
>> I changed the code to apply different alpha values for vdw and
>> electrostatics. Now I am able to e.g. calculate vdw with an alpha=1
>> (l-power linear or squared) and qq with alpha=0 (always linear, if alpha
>> != 0).
>> What I see are lincs errors after 40% of the sim-time in the upper case.
>> Is it because of the fact, that vdw are treated soft and qq hard?
>> With alpha=2 for qq it works, but still yields large fluctuations at
>> lambda=0 & 1.
>> Any suggestions?
>> Maik Goette, Dipl. Biol.
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical & computational biophysics department
>> Am Fassberg 11
>> 37077 Goettingen
>> Tel. : ++49 551 201 2310
>> Fax : ++49 551 201 2302
>> Email : mgoette[at]mpi-bpc.mpg.de
>> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
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