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
[EMAIL PROTECTED], p. 191 50673
------------------------------------------------------
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
[EMAIL PROTECTED]
------------------------------------------------------
;
; 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
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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