[gmx-users] grompp, energy minimization,, output file error

[Mark Abraham]

On 23/04/2010 8:52 AM, Moeed wrote:
> 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

Don't use -maxwarn unless you know why the warnings may be ignored.

> 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@!

It's a binary file. Don't try to read it with a text reader. GROMACS 
provides the gmxdump utility to get at the information, but that won't 
help you here.

> 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

Your system has a charge of 22061.57. This is because you've broken your 
[atoms] section. See below.

> processing coordinates...
>
> Warning: atom name 1 in HexaneModified.top and Hexane-stack.gro does not
> match (1 - C1)

Another symptom of the above.

> 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.

Another symptom.

> 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

You've omitted a whole field with the residue name. Thus grompp tries to 
fill the residue name with the atom name, and the atom name with the 
charge group number, etc., including the charge with the mass... The 
fact that grompp hasn't told you about this suggests either you 
suppressed a warning with -maxwarn, or grompp's cpp has (yet another) bug.

Mark