[gmx-users] Energy minimisation problem

Jussi Lehtola jussi.lehtola at helsinki.fi
Tue May 13 12:36:06 CEST 2008


Hi,



I have constructed topologies for methanol, ethanol, propanol and
butanol using x2top with the atomic coordinates from NIST Chemistry
WebBook. I have modified the topologies by putting the CH3s, CH2s and
OHs in their separate charge groups.

Now I have run into problems when trying to minimize the energy of the
configuration. I have used a system with 5000 molecules, with the box
size chosen to give an initial mass density of the order 500 kg/m^3
(which is less than the physical densities).

The system behaves really badly: the potential energy sticks to high
positive numbers (order of 10^6). I have tried with smaller densities
with no success. Sometimes the minimization gets energies of -10^8, but
the forces remain large. A few iterations after the potential energy
attains again positive values, and then converges to machine precision.

Increasing the step size doesn't help, neither does using another
minimizer (steep or l-bfgs): the system stays non-bonded.

Interestingly, if one generates the system using the -rot switch of
genconf, the potential increases some 10 orders of magnitude compared to
the default, -norot. 

What could be the problem?

Attachments: ethanol coordinates & topology
-- 
------------------------------------------------------
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50673
------------------------------------------------------
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi
------------------------------------------------------
-------------- next part --------------
;
;	File 'etanoli.top' was generated
;	By user: onbekend (0)
;	On host: onbekend
;	At date: Thu May  8 18:58:01 2008
;
;	This is your include topology file
;	Generated by x2top
;
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
ETH                 3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
     1   opls_157      1    Eth      C      1      -0.18     12.011   ; qtot -0.18
     2   opls_157      1    Eth      C      2      0.145     12.011   ; qtot -0.035
     3   opls_154      1    Eth      O      3     -0.683    15.9994   ; qtot -0.718
     4   opls_156      1    Eth      H      1       0.06      1.008   ; qtot -0.658
     5   opls_156      1    Eth      H      1       0.06      1.008   ; qtot -0.598
     6   opls_156      1    Eth      H      1       0.06      1.008   ; qtot -0.538
     7   opls_156      1    Eth      H      2       0.06      1.008   ; qtot -0.478
     8   opls_156      1    Eth      H      2       0.06      1.008   ; qtot -0.418
     9   opls_155      1    Eth      H      3      0.418      1.008   ; qtot 0

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1  1.520000e-01  4.000000e+05  1.520000e-01  4.000000e+05 
    1     4     1  1.100000e-01  4.000000e+05  1.100000e-01  4.000000e+05 
    1     5     1  1.090000e-01  4.000000e+05  1.090000e-01  4.000000e+05 
    1     6     1  1.100000e-01  4.000000e+05  1.100000e-01  4.000000e+05 
    2     3     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    2     7     1  1.100000e-01  4.000000e+05  1.100000e-01  4.000000e+05 
    2     8     1  1.110000e-01  4.000000e+05  1.110000e-01  4.000000e+05 
    3     9     1  9.470000e-02  4.000000e+05  9.470000e-02  4.000000e+05 

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     9     1 
    3     4     1 
    3     5     1 
    3     6     1 
    4     7     1 
    4     8     1 
    5     7     1 
    5     8     1 
    6     7     1 
    6     8     1 
    7     9     1 
    8     9     1 

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     4     1  1.100000e+02  4.000000e+02  1.100000e+02  4.000000e+02 
    2     1     5     1  1.120000e+02  4.000000e+02  1.120000e+02  4.000000e+02 
    2     1     6     1  1.110000e+02  4.000000e+02  1.110000e+02  4.000000e+02 
    4     1     5     1  1.080000e+02  4.000000e+02  1.080000e+02  4.000000e+02 
    4     1     6     1  1.070000e+02  4.000000e+02  1.070000e+02  4.000000e+02 
    5     1     6     1  1.080000e+02  4.000000e+02  1.080000e+02  4.000000e+02 
    1     2     3     1  1.080000e+02  4.000000e+02  1.080000e+02  4.000000e+02 
    1     2     7     1  1.110000e+02  4.000000e+02  1.110000e+02  4.000000e+02 
    1     2     8     1  1.110000e+02  4.000000e+02  1.110000e+02  4.000000e+02 
    3     2     7     1  1.100000e+02  4.000000e+02  1.100000e+02  4.000000e+02 
    3     2     8     1  1.100000e+02  4.000000e+02  1.100000e+02  4.000000e+02 
    7     2     8     1  1.070000e+02  4.000000e+02  1.070000e+02  4.000000e+02 
    2     3     9     1  1.070000e+02  4.000000e+02  1.070000e+02  4.000000e+02 

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    4     1     2     3     3  3.600000e+02  5.000000e+00  3.000000e+00  3.600000e+02  5.000000e+00  3.000000e+00 
    1     2     3     9     3  3.600000e+02  5.000000e+00  3.000000e+00  3.600000e+02  5.000000e+00  3.000000e+00 

-------------- next part --------------
Ethanol, ID: C64175
	9
    1Eth      C    1   0.103   0.088   0.098  0.0000  0.0000  0.0000
    1Eth      C    2   0.188   0.199   0.157  0.0000  0.0000  0.0000
    1Eth      O    3   0.319   0.148   0.174  0.0000  0.0000  0.0000
    1Eth      H    4   0.000   0.123   0.083  0.0000  0.0000  0.0000
    1Eth      H    5   0.099   0.000   0.163  0.0000  0.0000  0.0000
    1Eth      H    6   0.141   0.056   0.000  0.0000  0.0000  0.0000
    1Eth      H    7   0.190   0.287   0.091  0.0000  0.0000  0.0000
    1Eth      H    8   0.148   0.232   0.255  0.0000  0.0000  0.0000
    1Eth      H    9   0.371   0.218   0.211  0.0000  0.0000  0.0000
0.534785 0.534785 0.534785


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