On 6/14/13 4:58 PM, gromacs query wrote:
Dear All,
I have two different membrane systems (membrane with waters only) already
with me. So I dont need to add solvent molecules.
So to start with simulation I need box size (last line in gro file). I used
following command (for both cases):
editconf -f del.pdb -o del.gro -c -bt cubic
First case details:
system size : 10.707 11.077 7.493 (nm)
diameter : 14.737 (nm)
center : 6.928 6.932 6.936 (nm)
box vectors : 10.707 11.077 7.493 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume : 888.68 (nm^3)
shift : -1.574 -1.394 -3.190 (nm)
new center : 5.353 5.538 3.747 (nm)
I don't see how this is possible. You used -bt cubic, but you clearly (1) don't
want that, because the system is rectangular and (2) a cubic box is not
produced. Why even use editconf? Clearly the input .pdb file has correct box
vectors in it already and does not require any modification.
Second case details:
system size : 10.065 11.826 9.911 (nm)
diameter : 16.459 (nm)
center : 9.229 9.229 9.229 (nm)
box vectors : 18.459 18.459 18.459 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume :6289.31 (nm^3)
shift : 0.000 0.000 0.001 (nm)
new center : 9.229 9.229 9.229 (nm)
Here, there are probably erroneously large vectors written in the .pdb file
already.
-Justin
As I have solvents already so my box size as a rule should be (Maximum X -
Minimum X), (Maximum Y - Minimum Y), (Maximum Z - Minimum Z). This indeed I
found to be correct for my first case in which box dimensions in gro file =
10.707 11.077 7.493
But why in my second case box dimension in gro file = 18.459 18.459 18.459.
Surprisingly its is equal to Maximum X + Minimum X of my system and all are
same being 18.459. Rather it should be (Maximum X - Minimum X), (Maximum Y
- Minimum Y), (Maximum Z - Minimum Z) as in first case.
Also in VMD I saw gro files. In first case pbc box completely fits the
membrane water system but in second case pbc box is un-necessarily large as
it is using 18.459 18.459 18.459
I am confused why in second case it chose Maximum X + Minimum X unlike in
first case?
please suggest,
thanks,
Jiom
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
