Bing Bing wrote:
Hi!
Thanks for your suggestion on the tutorial. I will try it out.
I actually tried to use the starting structure without going through
editconf and alteration but it failed. Here's the error:
ERROR: The cut-off length is longer than half the shortest box vector or
longer than the smallest box diagonal element. Increase the box size or
decrease rlist.
I've tried on reducing the rlist but still failed. Please advice.
The POPC bilayer from Tieleman's site is a 6.2 x 6.1 nm box in x-y, and 6.9 nm
in z. How large are your cutoffs? You do realize that Gromacs uses nm, not
Angstrom, for these parameters, right?
According to the tutorial you suggested, we are suppose to use genbox to
solvate the membrane and remove those water manually by script that go
inside the membrane. Does this mean that I'm suppose to throw away the
water from the starting structure and resolvate it again?
I pointed you to the tutorial because you said you'd be running a membrane
protein. For a pure membrane, you do not need to remove water and re-solvate.
The POPC structure Tieleman provides is pre-equilibrated, so it should be fine
for a simulation of just the membrane.
-Justin
thanks again.
regards,
Bing
On Tue, Jun 23, 2009 at 11:28 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Bing Bing wrote:
Thanks for reply.
I've used editconf to define the box by issuing :-
editconf -f popc.pdb -o popc_box.gro -c -d 1.0 -bt cubic
Is this the correct way of using editconf?
This would be appropriate for a protein, but not a membrane. What
you're doing is defining a layer of nothingness around the
membrane/water system, which may have molecules split across
periodic boundaries. This could be the reason everything is blowing up.
Try running EM on the original, unaltered POPC from Tieleman's site.
And with this i proceed with grompp with the mdp file from
previous email followed by mdrun....
Actually the restraint is require in another system
(membrane+protein), i wanted to test it out in the this smaller
systme before using it in the complete systme.However, it failed.
Applying position restraints to every atom of a lipid in the
presence of a protein still serves little purpose. If you were to
attempt to energy-minimize such a system, the clashes (if any)
between the protein and lipids would go unresolved. Certainly
equilibrating with such restraints would be meaningless, as well.
If you're interested, hopefully the tutorial here will help:
http://oldwiki.gromacs.org/index.php/Membrane_Simulations
It is designed for membrane protein simulations.
-Justin
Thanks in advance
regards,
bing
On Tue, Jun 23, 2009 at 10:21 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
Bing Bing wrote:
Hi Justin,
I've tried with no restraint and the minimization stopped
at the
same time. I actually suspect that the restraint is not
working
at all. My top file is as below:-
#include "ffG53a6_lipid.itp"
#include "popc.itp"
#ifdef POSRES
#include "posres_popc.itp"
#endif
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif
[ system ]
; name
Pure POPC bilayer with 128 lipids 2460 water
[ molecules ]
; name number
POPC 128
SOL 2460
my posres_popc.itp is as below:-
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
.....
51 1 1000 1000 1000
52 1 1000 1000 1000
my mdp file as below :-
define = -DPOSRES
integrator = steep
emtol = 1000
emstep = 0.01
nsteps = 100
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
constraints = none
May i know that is the top, posres and also the mdp file
correctly done?
Well, they are syntactically correct, it seems. I see no
purpose in
restraining lipids during a minimization, however.
And by looking at the log file in the previous mail, is it
confirm that it manage to read the restraint file?
Can't tell. Your system is crashing instantly for some reason.
The starting structure is taken from Peter Tielemen
website and
what i did is editconf to make box and i didn't solvate
because
the starting structure come together with water. I'm not sure
this is the correct way of doing it. Please advice.
Please define "editconf to make box" - have you somehow
manipulated
the structure? That could be a source of error. The
structure that
Tieleman provides minimized for me with no problem when I used it
recently.
-Justin
Thanks in advance.
Bing
On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>> wrote:
Bing Bing wrote:
Hi! I'm a postgraduate student from Malaysia and
currently
facing energy minimization problem for my membrane
system.
I'm trying to perform energy minimization for an
empty POPC
membrane with position restraint on the lipid.
Minimization stop
due to inf Fmax. And I noticed that in the log file as
below:-
Initiating Steepest Descents
Max number of connections per atom is 25
Total number of connections is 84976
Max number of graph edges per atom is 4
Total number of graph edges is 22896
Going to use C-settle (2460 waters)
wo = 0.333333, wh =0.333333, wohh = 3, rc =
0.08165, ra =
0.0384897
rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH =
0.1633, dOH
= 0.1
Started Steepest Descents on node 0 Tue Jun 23
17:03:43 2009
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 100
Grid: 11 x 11 x 11 cells
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih.
Ryckaert-Bell.
Improper Dih.
1.64082e+05 1.71875e+04 4.06560e+03
6.45104e+03 8.36392e+03
LJ-14 Coulomb-14 LJ (SR) Coulomb
(SR) Coul. recip.
2.12067e-314 2.12067e-314 -1.58963e+04
-1.05392e+05 -1.15292e+05
Position Rest. Potential Pressure (bar)
0.00000e+00 -3.64297e+04 nan
>From the looks of some of these energies (i.e., LJ-14,
Coulomb-14), it looks like something is severely wrong
with your
starting structure, and applying position restraints
probably
isn't
helping.
Try the minimization without restraints and see if it
works.
Also, have you set the appropriate "define" line in
the .mdp
file,
corresponding to what is prescribed in the .top?
-Justin
-------------------------------------------------------
Program mdrun_d, VERSION 4.0.5
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each
particle
to a grid
based on its coordinates. If your system contains
collisions or
parameter
errors that give particles very high velocities
you might
end up
with some
coordinates being +-Infinity or NaN (not-a-number).
Obviously,
we cannot
put these on a grid, so this is usually where we
detect those
errors.
Make sure your system is properly energy-minimized and
that the
potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been
within [
0 .. 1331 ]
the position restraint energy is 0 as highlighted.
Here's the
position restraint file :-
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 5000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
10 1 1000 1000 1000
......
whereby the restraint energy is 1000kcal/mol in x,
y and z
plane. In the log file the position restraint
energy is
stated
as 0.0000e+00 (as highlighted above).
I think that the position restraint is not working
fine
here. Is
there anyways to solve this? did I miss out
something here?
I would be grateful if anyone can advice me on this.
------------------------------------------------------------------------
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
<http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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