[gmx-users] grompp, energy minimization,, output file error
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 23 01:05:33 CEST 2010
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
>
>
> 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@!
>
>
A .tpr file is binary. You won't be able to read it.
> 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
>
This line is very concerning. You have a net charge in excess of +22000!
Something is badly broken in your topology.
>
>
> processing coordinates...
>
> Warning: atom name 1 in HexaneModified.top and Hexane-stack.gro does not
> match (1 - C1)
These errors all indicate that you either have something out of order in your
[molecules] directive (it has to match the order of the molecules in the
coordinate file) or you have an improperly-formatted coordinate file.
<snip>
>
> 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.
>
See the manual for the group concept. Large charge groups can cause bad
electrostatics artifacts.
> 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.
>
There is also very little justification for using plain cutoffs. Heed the
warning and use a more reasonable (and modern) setting.
<snip>
> [ 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
>
All of your atoms are in the same charge group. This is why you see the note
above. Look at some basic building blocks for examples of more appropriate
settings, or read the note again - it tells you how to more reasonably group
your charges.
You also don't have any residue names in your topology, which is probably why
you see the ridiculous net charge; it is not being processed properly. Go
through some basic tutorial material to see a proper topology format generated
by pdb2gmx.
<snip>
>
>
> **************************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
Here is the cause of your mismatching names. Your .gro file is not correctly
formatted, either. Like your topology, it also doesn't contain residue names.
See here:
http://manual.gromacs.org/current/online/gro.html
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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