Dear Ignacio,
> I am trying to compare a thermodynamic integration done with PME vs one
> without PME, both in vacuum. But I am obtaining strange results. Maybe
This does not make any sense. The purpose of PME (and I assume by with PME
you mean using regular Ewald , or do you mean a simple direct space cutoff?)
is to give you long range electrostatics. While you can certainly build your
system without solvent and put a box around it and run PME it certainly will
not be 'in vacuum' since you will have all the images of your protein
present. I think you need to think carefully here about what it is you want
to simulate and what you actually are / can simulate.
> somebody can point some error I am making inadvertently. So here is the
> procedure I follow:
>
> 1) Build a system consisting only of a ligand, using xleap, and
> generate
> from there the coordinate and parameter files. I'll use these two files
> to
> run the ligand in vacuum, no PME, TI.
Yes this is a vacuum simulation.
> 2) Take the coordinate file (restart format) in previous step and add a
> line
> at the end of it, containing size and angles of the box.
You should NOT do this, since you need a corresponding prmtop file that is
also setup for periodic boundaries, not just the coordinate file. Use the
setbox command in xleap and then save your prmtop and inpcrd file which will
now be setup for periodic simulations (see caveat above about this NOT being
a vacuum simulation).
> 3) Take the parameter file from step 1), and add three flags,
> SOLVENT_POINTERS, ATOMS_PER_MOLECULE and BOX_DIMENSIONS.
This is hacking and will lead to a whole world of pain. Better to use the
setbox option.
Note, in both cases you probably want to set cutoff to be larger than your
protein since otherwise you will have to deal with the fact you have erfc
present in the PME case but not in the vacuum case. Note also that the
result you will get with the PME case will be dependent on the size of your
box which is this case is effectively arbitrary, hence I am not sure what
you will actually learn of value from these calculations. It certainly
deserves careful thinking about.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Mon May 23 2011 - 14:00:02 PDT
