[gmx-users] non zero charge in topolgy
Moeed
lecielll at googlemail.com
Tue May 11 05:18:42 CEST 2010
Dear experts,
1- I am trying to produce tpr file for EM (there is one hexane molecule in
my system). It seems top file has non zero charge. could you please help me
how to deal with this problem.
2-To run the simulation for one single hexane molecule what should the box
size be? it is- box 3 3 3 -angles 90 90 90 now!
3- Also in the top file (generated by pdb2gmx) the molecules name that
automatically appears is "protein". I dont have water molecule in my sys.
Can I change the name of the molecule and remove water topology by hand? I
dont know why water topoly is included....
Thank you :)
*********************************************************em.mdp
title = Hexane
cpp = /lib/cpp
define = -DFLEX_SPC
constraints = all-bonds
integrator = steep
dt = 0.002 ; ps !
nsteps = 200
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
*****************************
output.grompp_em
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
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
Opening library file /chem_soft/gromacs/share/gromacs/top/spc.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein'
NOTE 1 [file Hexane-PRODRG.top, line 221]:
System has non-zero total charge: 2.400000e-01
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 20 elements
Making dummy/rest group for Acceleration containing 20 elements
Making dummy/rest group for Freeze containing 20 elements
Making dummy/rest group for Energy Mon. containing 20 elements
Making dummy/rest group for VCM containing 20 elements
Number of degrees of freedom in T-Coupling group rest is 38.00
Making dummy/rest group for User1 containing 20 elements
Making dummy/rest group for User2 containing 20 elements
Making dummy/rest group for XTC containing 20 elements
Making dummy/rest group for Or. Res. Fit containing 20 elements
Making dummy/rest group for QMMM containing 20 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 2 [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 2 notes
gcq#276: "Yeah, uh uh, Neil's Head !" (Neil)
:-) 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: 1 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
This run will generate roughly 0 Mb of data
***********************************************************************************************
;
; File 'Hexane-PRODRG.top' was generated
; By user: moeed (500)
; On host: moeed-desktop
; At date: Mon May 10 23:01:58 2010
;
; This is your topology file
; "Never Get a Chance to Kick Ass" (The Amps)
;
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Protein 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
0.18
10 opls_140 1 HEX H32 3 0.06 1.008 ; qtot
0.24
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
0.18
13 opls_140 1 HEX H42 4 0.06 1.008 ; qtot
0.24
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
0.18
16 opls_140 1 HEX H52 5 0.06 1.008 ; qtot
0.24
17 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot
0.06
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
0.18
20 opls_140 1 HEX H63 6 0.06 1.008 ; qtot
0.24
[ 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
Protein
[ molecules ]
; Compound #mols
Protein 1
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