[gmx-users] Problem in energy minimization for a empty membrane system
Bing Bing
jarbing09 at gmail.com
Tue Jun 23 15:25:05 CEST 2009
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?
And by looking at the log file in the previous mail, is it confirm that it
manage to read the restraint file?
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.
Thanks in advance.
Bing
On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul <jalemkul at vt.edu> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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