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]>> 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]>>> 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.
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
-- ========================================
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
