[gmx-users] Break down of total energy

Moeed lecielll at googlemail.com
Fri May 21 20:50:14 CEST 2010


Hello Justin,

As for exclusions, in the manual I see 1-4 interactions refer to carbon
atoms on the backbone. I do not know if it makes sense if I enter a number
more than 5 (hexane has only 6 carbons), However, I did so and I changed
nrexcl from default value of 3 to 19 ( to exlude all interactions between
all C and H atoms!) but I got the following message after grompp em step:


checking input for internal consistency...
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 19 bonded neighbours molecule type 'Hexane'

-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: smalloc.c, line: 147

Fatal error:
Not enough memory. Failed to calloc 78089438 elements of size 8 for s
(called from file topexcl.c, line 161)
-------------------------------------------------------

I also tried another approach (although I am almost sure this is not the
proper way of excluding ALL interactions as in this way I think I am
excluding atom 1 and all other atoms only!) and added exclusions directive
as you see below in top file


; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Hexane              3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
     1   opls_157      1    HEX     C1      1      -0.18     12.011   ; qtot
-0.18
     2   opls_140      1    HEX    H11      1       0.06      1.008   ; qtot
-0.12
     3   opls_140      1    HEX    H12      1       0.06      1.008   ; qtot
-0.06
     4   opls_140      1    HEX    H13      1       0.06      1.008   ; qtot
0
     5   opls_158      1    HEX     C2      2      -0.12     12.011   ; qtot
-0.12
     6   opls_140      1    HEX    H21      2       0.06      1.008   ; qtot
-0.06
     7   opls_140      1    HEX    H22      2       0.06      1.008   ; qtot
0
     8   opls_158      1    HEX     C3      3      -0.12     12.011   ; qtot
-0.12
     9   opls_140      1    HEX    H31      3       0.06      1.008   ; qtot
-0.06
    10   opls_140      1    HEX    H32      3       0.06      1.008   ; qtot
0
    11   opls_158      1    HEX     C4      4      -0.12     12.011   ; qtot
-0.12
    12   opls_140      1    HEX    H41      4       0.06      1.008   ; qtot
-0.06
    13   opls_140      1    HEX    H42      4       0.06      1.008   ; qtot
0
    14   opls_158      1    HEX     C5      5      -0.12     12.011   ; qtot
-0.12
    15   opls_140      1    HEX    H51      5       0.06      1.008   ; qtot
-0.06
    16   opls_140      1    HEX    H52      5       0.06      1.008   ; qtot
0
    17   opls_157      1    HEX     C6      6      -0.18     12.011   ; qtot
-0.18
    18   opls_140      1    HEX    H61      6       0.06      1.008   ; qtot
-0.12
    19   opls_140      1    HEX    H62      6       0.06      1.008   ; qtot
-0.06
    20   opls_140      1    HEX    H63      6       0.06      1.008   ; qtot
0

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1
    1     3     1
    1     4     1
    1     5     1
    5     6     1
    5     7     1
    5     8     1
    8     9     1
    8    10     1
    8    11     1
   11    12     1
   11    13     1
   11    14     1
   14    15     1
   14    16     1
   14    17     1
   17    18     1
   17    19     1
   17    20     1

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     9     1
    1    10     1
    1    11     1
    2     6     1
    2     7     1
    2     8     1
    3     6     1
    3     7     1
    3     8     1
    4     6     1
    4     7     1
    4     8     1
    5    12     1
    5    13     1
    5    14     1
    6     9     1
    6    10     1
    6    11     1
    7     9     1
    7    10     1
    7    11     1
    8    15     1
    8    16     1
    8    17     1
    9    12     1
    9    13     1
    9    14     1
   10    12     1
   10    13     1
   10    14     1
   11    18     1
   11    19     1
   11    20     1
   12    15     1
   12    16     1
   12    17     1
   13    15     1
   13    16     1
   13    17     1
   15    18     1
   15    19     1
   15    20     1
   16    18     1
   16    19     1
   16    20     1

[ angles ]
;  ai    aj    ak funct            c0            c1            c2
c3
    2     1     3     1
    2     1     4     1
    2     1     5     1
    3     1     4     1
    3     1     5     1
    4     1     5     1
    1     5     6     1
    1     5     7     1
    1     5     8     1
    6     5     7     1
    6     5     8     1
    7     5     8     1
    5     8     9     1
    5     8    10     1
    5     8    11     1
    9     8    10     1
    9     8    11     1
   10     8    11     1
    8    11    12     1
    8    11    13     1
    8    11    14     1
   12    11    13     1
   12    11    14     1
   13    11    14     1
   11    14    15     1
   11    14    16     1
   11    14    17     1
   15    14    16     1
   15    14    17     1
   16    14    17     1
   14    17    18     1
   14    17    19     1
   14    17    20     1
   18    17    19     1
   18    17    20     1
   19    17    20     1

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1
c2            c3            c4            c5
    2     1     5     6     3
    2     1     5     7     3
    2     1     5     8     3
    3     1     5     6     3
    3     1     5     7     3
    3     1     5     8     3
    4     1     5     6     3
    4     1     5     7     3
    4     1     5     8     3
    1     5     8     9     3
    1     5     8    10     3
    1     5     8    11     3
    6     5     8     9     3
    6     5     8    10     3
    6     5     8    11     3
    7     5     8     9     3
    7     5     8    10     3
    7     5     8    11     3
    5     8    11    12     3
    5     8    11    13     3
    5     8    11    14     3
    9     8    11    12     3
    9     8    11    13     3
    9     8    11    14     3
   10     8    11    12     3
   10     8    11    13     3
   10     8    11    14     3
    8    11    14    15     3
    8    11    14    16     3
    8    11    14    17     3
   12    11    14    15     3
   12    11    14    16     3
   12    11    14    17     3
   13    11    14    15     3
   13    11    14    16     3
   13    11    14    17     3
   11    14    17    18     3
   11    14    17    19     3
   11    14    17    20     3
   15    14    17    18     3
   15    14    17    19     3
   15    14    17    20     3
   16    14    17    18     3
   16    14    17    19     3
   16    14    17    20     3

; Include Position restraint file
;#ifdef POSRES
;#include "posre.itp"
;#endif

; Include water topology
;#include "spc.itp"

;#ifdef POSRES_WATER
; Position restraint for each water oxygen
;[ position_restraints ]
;  i funct       fcx        fcy        fcz
 ;  1    1       1000       1000       1000
;#endif

; Include generic topology for ions
;#include "ions.itp"

*[ exclusions ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
*
[ system ]
; Name
Hexane

[ molecules ]
; Compound        #mols
Hexane              125

*************************************************


Then I used the following comamnds:

grompp -f em -c Hexane-Stack125.gro -p Hexane-Stack125-nrexcl19.top -o
Hexane-Stack125_em >& output.grompp_em


mdrun -s Hexane-Stack125_em -o Hexane-Stack125_em -c Hexane-Stack125_b4pr -v
>& output.mdrun_em


 grompp -f md13 -c Hexane-Stack125_b4pr -p Hexane-Stack125-nrexcl19.top -o
Hexane-Stack125_md >& output.grompp_md


mdrun -rerun Hexane-Stack125_md.tpr.trr


-------------------------------------------------------
Program mdrun, VERSION 4.0.7
Source code file: gmxfio.c, line: 737

Can not open file:
topol.tpr


**********************************************************************************************



Do I need to do this as:

[exclusions]
1 2
1 3
1 4
...
1 20
2 3
3 4
.
.
3 20
.

.


since this involves tedious work I would like you to help me with first
approach (nrexcl in moleculetype) and let me know what wrong is..


Thank you,
moeed
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100521/a4a16bc7/attachment.html>


More information about the gromacs.org_gmx-users mailing list