On 10/18/2012 11:53 AM, Justin Lemkul wrote:
On 10/18/12 2:43 PM, klexa wrote:
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes
that are not
standard cubes. I'm trying to run a membrane simulation where a cyclic
undecapeptide is inserted into the membrane and I want the water layer to be
sufficiently thick that if it were pulled, the peptide could be
fully solvated
by the water. To avoid having an enormous box of membrane and
water, I have an
orthorhombic box containing my peptide and bilayer. It minimizes
alright with
Gromacs, but when I go to equilibrate it it fails because it's too
skewed to be
a triclinic box. I've tried modifying the box with editconf and
converting it to
a rhombic dodecahedron, sort of like the manual suggests for a
membrane system.
I'm not sure that even that is sensible since it seems like I would
be losing
content that way, yet nothing is clipped, and I did this after
using trjconv to
remove any periodicity from my prior simulation of this system (in
Desmond) but
doing so gives me a starting potential energy of NaN for the new
system that I
obviously cannot work around. Is what I am trying to do even
possible? If it is,
it seems like there is probably a better way than the way I chose, so if you
have any suggestions, I would be greatly appreciative.
I have never produced a membrane system with a hexagonal
cross-section like the manual describes. The most straightforward
approach in my mind is simply a rectangular box. It will save you a
ton of headaches.
Okay, yes, it does seem much simpler. But if I can indeed just use a
rectangular box like 7.7 7.7 10.5, why does Gromacs fail with the
"triclinic too skewed" error?
{ -1.75e+25 0 -0
-0 -1.75e+25 -0
-0 -0 -2.49e+25}
Maybe it's just related to this force field mixing, but otherwise, if
I should be able to proceed with a rectangular box, does that need to
be specified somewhere outside of when I use genbox to solvate my
system with -box 7.7 7.7 10.5?
I'm trying to run this simulation with AMBER FF99SB parameters for
the peptide,
Tieleman's lipid parameters for POPC, and SPCE waters, so just as a sanity
check, is it reasonable to consider a system like that?
I don't know how this would even run. The AMBER protein force field
and Berger lipid paramters use different combination rules, and I
have never seen a demonstration that one can use them together. It
is most straightforward to use a Gromos force field or OPLS-AA with
modifications to account for the changes in combination rules.
Great, I'm glad to hear it as I was skeptical too. I can tell you that
after 2 months of trying to get a system like working, it still hasn't
succeeded in any form, so the odds are not in its favor.
-Justin
Thank you!
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