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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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