[gmx-users] grompp, energy minimization,, output file error
Moeed
lecielll at googlemail.com
Fri Apr 23 00:52:18 CEST 2010
Dear gmx users,
I am trying to run grompp program to preprocess the input files. input gro
file contains coordinates of a stack of hexane molecules (256 molecules).
grompp -f em -c Hexane-stack.gro -p HexaneModified.top -o Hexane_em -maxwarn
30 >& output.grompp_em
my problem is that output: Hexane_em.tpr contains strange notations:
éxÕ@!`A‰7KÇ?ý"Ðå`A‰@!(r° Äœ@(LÌÌÌÌÍ?û Iº^5@!O\(õ @(LÌÌÌÌÍ?ù n— Oß@!
¾vÈ´9@(LÌÌÌÌÍ?öí‘hr°!@!F§ï
²-@(LÌÌÌÌÍ?ôýó¶E¡Ë@!
output.grompp_em:
GNU nano 2.0.9 File:
output.grompp_em
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
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 3 bonded neighbours molecule type 'HEX'
NOTE 1 [file HexaneModified.top, line 163]:
System has non-zero total charge: 2.206157e+04
processing coordinates...
Warning: atom name 1 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C1)
Warning: atom name 2 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C2)
Warning: atom name 3 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C3)
Warning: atom name 4 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C4)
Warning: atom name 5 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C5)
Warning: atom name 6 in HexaneModified.top and Hexane-stack.gro does not
match (1 - C6)
Warning: atom name 7 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H1)
Warning: atom name 8 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H2)
Warning: atom name 9 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H3)
Warning: atom name 10 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H4)
Warning: atom name 11 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H5)
Warning: atom name 12 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H6)
Warning: atom name 13 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H7)
Warning: atom name 14 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H8)
Warning: atom name 15 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H9)
Warning: atom name 16 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H10)
Warning: atom name 17 in HexaneModified.top and Hexane-stack.gro does not
match (1 - H11)
WARNING 1 [file HexaneModified.top, line 163]:
5120 non-matching atom names
atom names from HexaneModified.top will be used
atom names from Hexane-stack.gro will be ignored
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
NOTE 2 [file HexaneModified.top, line unknown]:
The largest charge group contains 20 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
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 5120 elements
Making dummy/rest group for Acceleration containing 5120 elements
Making dummy/rest group for Freeze containing 5120 elements
Making dummy/rest group for Energy Mon. containing 5120 elements
Making dummy/rest group for VCM containing 5120 elements
Number of degrees of freedom in T-Coupling group rest is 15357.00
Making dummy/rest group for User1 containing 5120 elements
Making dummy/rest group for User2 containing 5120 elements
Making dummy/rest group for XTC containing 5120 elements
Making dummy/rest group for Or. Res. Fit containing 5120 elements
Making dummy/rest group for QMMM containing 5120 elements
T-Coupling has 1 element(s): rest
Energy Mon. has 1 element(s): rest
Checking consistency between energy and charge groups...
NOTE 3 [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 were 3 notes
There was 1 warning
Back Off! I just backed up Hexane_em.tpr to ./#Hexane_em.tpr.1#
gcq#312: "Move about like a Scientist, lay down, get kissed" (Red Hot Chili
Peppars)
processing topology...
Analysing residue names:
There are: 256 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
This run will generate roughly 1 Mb of data
*********************************************************************************************************************
em.mdp file I use:
;title = cpeptide
cpp = /lib/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 100
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
****************************topology file:
;
; File 'Hexane.top' was generated
; By user: moeed (500)
; On host: moeed-desktop
; At date: Thu Apr 8 13:51:19 2010
;
; This is your include topology file
; Generated by x2top
;
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
HEX 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_157 1 C1 1 -0.18 12.011 ; qtot
-0.18
2 opls_158 1 C2 1 -0.12 12.011 ; qtot
-0.3
3 opls_158 1 C3 1 -0.12 12.011 ; qtot
-0.42
4 opls_158 1 C4 1 -0.12 12.011 ; qtot
-0.54
5 opls_158 1 C5 1 -0.12 12.011 ; qtot
-0.66
6 opls_157 1 C6 1 -0.18 12.011 ; qtot
-0.84
7 opls_140 1 H1 1 0.06 1.008 ; qtot
-0.78
8 opls_140 1 H2 1 0.06 1.008 ; qtot
-0.72
9 opls_140 1 H3 1 0.06 1.008 ; qtot
-0.66
10 opls_140 1 H4 1 0.06 1.008 ; qtot
-0.6
11 opls_140 1 H5 1 0.06 1.008 ; qtot
-0.54
12 opls_140 1 H6 1 0.06 1.008 ; qtot
-0.48
13 opls_140 1 H7 1 0.06 1.008 ; qtot
-0.42
14 opls_140 1 H8 1 0.06 1.008 ; qtot
-0.36
15 opls_140 1 H9 1 0.06 1.008 ; qtot
-0.3
16 opls_140 1 H10 1 0.06 1.008 ; qtot
-0.24
17 opls_140 1 H11 1 0.06 1.008 ; qtot
-0.18
18 opls_140 1 H12 1 0.06 1.008 ; qtot
-0.12
19 opls_140 1 H13 1 0.06 1.008 ; qtot
-0.06
20 opls_140 1 H14 1 0.06 1.008 ; qtot
0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
1 18 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
1 19 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
1 20 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
2 3 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
2 16 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
2 17 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
3 4 1 1.540000e-01 4.000000e+05 1.540000e-01 4.000000e+05
3 14 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
3 15 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
4 5 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
4 12 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
4 13 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
5 6 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
5 10 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
5 11 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
6 7 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
6 8 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
6 9 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 14 1
1 15 1
2 5 1
2 12 1
2 13 1
3 6 1
3 10 1
3 11 1
3 18 1
3 19 1
3 20 1
4 7 1
4 8 1
4 9 1
4 16 1
4 17 1
5 14 1
5 15 1
6 12 1
6 13 1
7 10 1
7 11 1
8 10 1
8 11 1
9 10 1
9 11 1
10 12 1
10 13 1
11 12 1
11 13 1
12 14 1
12 15 1
13 14 1
13 15 1
14 16 1
14 17 1
15 16 1
15 17 1
16 18 1
16 19 1
16 20 1
17 18 1
17 19 1
17 20 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 18 1 1.120000e+02 4.000000e+02 1.120000e+02
4.000000e+02
2 1 19 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
2 1 20 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
18 1 19 1 1.070000e+02 4.000000e+02 1.070000e+02
4.000000e+02
18 1 20 1 1.070000e+02 4.000000e+02 1.070000e+02
4.000000e+02
19 1 20 1 1.080000e+02 4.000000e+02 1.080000e+02
4.000000e+02
1 2 3 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
1 2 16 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
1 2 17 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
3 2 16 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
3 2 17 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
16 2 17 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
2 3 4 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
2 3 14 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
2 3 15 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
4 3 14 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
4 3 15 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
14 3 15 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
3 4 5 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
3 4 12 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
3 4 13 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
5 4 12 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
5 4 13 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
12 4 13 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
4 5 6 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
4 5 10 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
4 5 11 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
6 5 10 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
6 5 11 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
10 5 11 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
5 6 7 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
5 6 8 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
5 6 9 1 1.120000e+02 4.000000e+02 1.120000e+02
4.000000e+02
7 6 8 1 1.080000e+02 4.000000e+02 1.080000e+02
4.000000e+02
7 6 9 1 1.070000e+02 4.000000e+02 1.070000e+02
4.000000e+02
8 6 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
18 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 4 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
2 3 4 5 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
3 4 5 6 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
4 5 6 7 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
[ system ]
; Name
HEX
[ molecules ]
; Compound #mols
HEX 256
**************************the first molecule in gro file:(there are 256)
Go Rough, Oppose Many Angry Chinese Serial killers
5120
1 C1 1 1.821 1.479 1.500 0.0000 0.0000 0.0000
1 C2 2 1.688 1.555 1.500 0.0000 0.0000 0.0000
1 C3 3 1.567 1.462 1.500 0.0000 0.0000 0.0000
1 C4 4 1.433 1.538 1.500 0.0000 0.0000 0.0000
1 C5 5 1.312 1.445 1.500 0.0000 0.0000 0.0000
1 C6 6 1.179 1.521 1.500 0.0000 0.0000 0.0000
1 H1 7 1.170 1.584 1.412 0.0000 0.0000 0.0000
1 H2 8 1.170 1.584 1.588 0.0000 0.0000 0.0000
1 H3 9 1.094 1.453 1.500 0.0000 0.0000 0.0000
1 H4 10 1.316 1.380 1.587 0.0000 0.0000 0.0000
1 H5 11 1.316 1.380 1.413 0.0000 0.0000 0.0000
1 H6 12 1.429 1.603 1.587 0.0000 0.0000 0.0000
1 H7 13 1.429 1.603 1.413 0.0000 0.0000 0.0000
1 H8 14 1.571 1.397 1.587 0.0000 0.0000 0.0000
1 H9 15 1.571 1.397 1.413 0.0000 0.0000 0.0000
1 H10 16 1.684 1.620 1.587 0.0000 0.0000 0.0000
1 H11 17 1.684 1.620 1.413 0.0000 0.0000 0.0000
1 H12 18 1.906 1.547 1.500 0.0000 0.0000 0.0000
1 H13 19 1.830 1.416 1.412 0.0000 0.0000 0.0000
1 H14 20 1.830 1.416 1.588 0.0000 0.0000 0.0000
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