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:
é...@!`a‰7kÇ?ý"Ðå`a...@!(r° Äœ@(LÌÌÌÌÍ?û i�...@!o\(õ @(LÌÌÌÌÍ?ù n— o...@!
¾vÈ´9@(lÌÌÌÌÍ?öí‘hr...@!f§ï ²-@(lÌÌÌÌÍ?ôýó¶e�...@!
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
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