Dear experts,
I am trying to exclude all nonbonded interaction on hexane molecule.
1-For the md -rerun command I do not know how to get the input XTC file. the
program is expecting rerun.xtc
mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o
ORIGINAL-Trajectory-NOexcl.tpr* -c Hexane-Stack125_after_md -v >&
output.mdrun_m
2-Can you please check exclsusions directive in top file. I have used also
nrexcl 5 in molecule top. does this make sense given that I have defined all
the possible exclusions in 19 lines.
********************grompp em :
*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 5 bonded neighbours molecule type 'Hexane'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
Making dummy/rest group for T-Coupling containing 2500 elements
Making dummy/rest group for Acceleration containing 2500 elements
Making dummy/rest group for Freeze containing 2500 elements
Making dummy/rest group for Energy Mon. containing 2500 elements
Making dummy/rest group for VCM containing 2500 elements
Number of degrees of freedom in T-Coupling group rest is 5122.00
Making dummy/rest group for User1 containing 2500 elements
Making dummy/rest group for User2 containing 2500 elements
Making dummy/rest group for XTC containing 2500 elements
Making dummy/rest group for Or. Res. Fit containing 2500 elements
Making dummy/rest group for QMMM containing 2500 elements
T-Coupling has 1 element(s): rest
Energy Mon. has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
NOTE 1 [file em.mdp, line unknown]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
writing run input file...
There was 1 note
Back Off! I just backed up Hexane-Stack125_em.tpr to
./#Hexane-Stack125_em.tpr.4#
gcq#320: "Do You Have Sex Maniacs or Schizophrenics or Astrophysicists in
Your Family?" (Gogol Bordello)
:-) G R O M A C S (-:
Getting the Right Output Means no Artefacts in Calculating Stuff
:-) VERSION 4.0.7 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (double precision) (-:
processing topology...
turning all bonds into constraints...
Analysing residue names:
There are: 125 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
This run will generate roughly 1 Mb of data
********************************************************************output
md_em:
teepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 200
Step= 0, Dmax= 1.0e-02 nm, Epot= -2.41657e+03 Fmax= 1.96636e+02, atom=
1189
writing lowest energy coordinates.
Back Off! I just backed up Hexane-Stack125_b4pr.gro to
./#Hexane-Stack125_b4pr.gro.4#
Steepest Descents converged to Fmax < 1000 in 1 steps
Potential Energy = -2.41656779590808e+03
Maximum force = 1.96635853696765e+02 on atom 1189
Norm of force = 1.37247833599652e+02
******************************************************************************************************out
put grompp md
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 5 bonded neighbours molecule type 'Hexane'
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
Making dummy/rest group for Acceleration containing 2500 elements
Making dummy/rest group for Freeze containing 2500 elements
Making dummy/rest group for Energy Mon. containing 2500 elements
Making dummy/rest group for VCM containing 2500 elements
Number of degrees of freedom in T-Coupling group HEX is 5122.00
Making dummy/rest group for User1 containing 2500 elements
Making dummy/rest group for User2 containing 2500 elements
Making dummy/rest group for XTC containing 2500 elements
Making dummy/rest group for Or. Res. Fit containing 2500 elements
Making dummy/rest group for QMMM containing 2500 elements
T-Coupling has 1 element(s): HEX
Energy Mon. has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
Estimate for the relative computational load of the PME mesh part: 0.13
writing run input file...
There was 1 note
Back Off! I just backed up Hexane-Stack125_md.tpr to
./#Hexane-Stack125_md.tpr.1#
gcq#190: "Load Up Your Rubber Bullets" (10 CC)
:-) G R O M A C S (-:
Gravel Rubs Often Many Awfully Cauterized Sores
:-) VERSION 4.0.7 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (double precision) (-:
processing topology...
turning all bonds into constraints...
Analysing residue names:
There are: 125 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 42x21x21, spacing 0.119 0.119 0.119
This run will generate roughly 65 Mb of data
***********************************************************************
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Hexane 5
[ 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
[ exclusions ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
7 8 9 10 11 12 13 14 15 16 17 18 19 20
8 9 10 11 12 13 14 15 16 17 18 19 20
9 10 11 12 13 14 15 16 17 18 19 20
10 11 12 13 14 15 16 17 18 19 20
11 12 13 14 15 16 17 18 19 20
12 13 14 15 16 17 18 19 20
13 14 15 16 17 18 19 20
14 15 16 17 18 19 20
15 16 17 18 19 20
16 17 18 19 20
17 18 19 20
18 19 20
19 20
[ 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"
[ system ]
; Name
Hexane
[ molecules ]
; Compound #mols
Hexane 125
--
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