[gmx-users] non zero charge in topolgy

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue May 11 05:28:59 CEST 2010


Your problem is here:

      8   opls_158      1    HEX     C3      3       0.12     12.011   ; qtot
0.12

As for the other questions, I could answer them but I think that it  
would preclude you from pursuing the more useful solution: read the  
manual and read some papers and do some tutorials.

Chris.

-- original message --

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)

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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

      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

      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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