On 10/18/12 3:04 PM, klexa wrote:
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}
The values shown here indicate that the unit cell has gone completely haywire.
They clearly bear no resemblance to the values you hope to use.
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 find it better to use editconf -box to build the system and simultaneously
position the molecules within the unit cell with -center. Then follow with
solvation.
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.
There is a tutorial available explaining the force field logic, if you're
interested.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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