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Bug #1667

Updated by Mark Abraham about 6 years ago

I notice when i tryed to remove solvent from tpr file and write new one with gmx convert-tpr that output file always contain all molecules merged, so effective number of mols are 1. However in this case output should contain 10 mols (9 proteins and 1 rna)

<pre>
gmx convert-tpr -s hk_162_39_ring9_rna.md_npt.tpr -nsteps -1 -o tmp.tpr -n index.ndx
GROMACS: gmx convert-tpr, VERSION 5.0.4
Executable: /usr/bin/gmx
Library dir: /usr/share/gromacs/top
Command line:
gmx convert-tpr -s hk_162_39_ring9_rna.md_npt.tpr -nsteps -1 -o tmp.tpr -n index.ndx

Reading toplogy and stuff from hk_162_39_ring9_rna.md_npt.tpr
Reading file hk_162_39_ring9_rna.md_npt.tpr, VERSION 5.1-dev-20140712-06ff230-dirty-unknown (single precision)
Setting nsteps to -1
Group 0 ( System) has 644440 elements
Group 1 ( Protein) has 70200 elements
Group 2 ( Protein-H) has 35289 elements
Group 3 ( C-alpha) has 4482 elements
Group 4 ( Backbone) has 13446 elements
Group 5 ( MainChain) has 17937 elements
Group 6 ( MainChain+Cb) has 22050 elements
Group 7 ( MainChain+H) has 22275 elements
Group 8 ( SideChain) has 47925 elements
Group 9 ( SideChain-H) has 17352 elements
Group 10 ( Prot-Masses) has 70200 elements
Group 11 ( non-Protein) has 574240 elements
Group 12 ( RNA) has 5579 elements
Group 13 ( NA) has 272 elements
Group 14 ( CL) has 195 elements
Group 15 ( Water) has 568194 elements
Group 16 ( SOL) has 568194 elements
Group 17 ( non-Water) has 76246 elements
Group 18 ( Ion) has 467 elements
Group 19 ( NA) has 272 elements
Group 20 ( CL) has 195 elements
Group 21 ( Water_and_ions) has 568661 elements
Group 22 ( Protein_RNA) has 75779 elements
Select a group: 22
Selected 22: 'Protein_RNA'
Will write subset Protein_RNA of original tpx containing 75779 atoms
Reduced block cgs from 644440 to 75779 index-, 644440 to 75779 a-entries
Reduced block mols from 189875 to 10 index-, 644440 to 75779 a-entries
Reduced block excls from 644440 to 75779 index-, 2605914 to 900865 a-entries
Reduced ilist ANGLES from 138078 to 138078 entries
Reduced ilist PDIHS from 208589 to 208589 entries
Reduced ilist PIDIHS from 15444 to 15444 entries
Reduced ilist LJ14 from 197721 to 197721 entries
Reduced ilist CONSTR from 76744 to 76744 entries
Reduced ilist SETTLE from 189398 to 0 entries
Writing statusfile with starting step 0 and length -1 steps...
time 0.000 and length -0.002 ps

alexxy@mdstore ~/Models/np/hk_162_39_ring9_rna/312K $ gmxcheck -s1 tmp.tpr -m /tmp/
GROMACS: gmx check, VERSION 5.0.4
Executable: /usr/bin/gmx
Library dir: /usr/share/gromacs/top
Command line:
gmxcheck -s1 tmp.tpr -m /tmp/

Reading file tmp.tpr, VERSION 5.0.4 (single precision)

Back Off! I just backed up /tmp/.tex to /tmp/#.tex.2#

gcq#147: "I'm An Oakman" (Pulp Fiction)

alexxy@mdstore ~/Models/np/hk_162_39_ring9_rna/312K $ cat /tmp/.tex
\section{Methods}
\subsection{Simulation system}
A system of 1 molecules (75779 atoms) was simulated.

\subsection{Simulation settings}
A total of -2e-06 ns were simulated with a time step of 2 fs.
Neighbor searching was performed every 500 steps.
The PME algorithm was used for electrostatic interactions.
with a cut-off of 1.2 nm.
A reciprocal grid of 216 x 216 x 96 cells was used with 4th order B-spline interpolation.
A single cut-off of 2.485 was used for Van der Waals interactions.
Temperature coupling was done with the Nose-Hoover algorithm.
Pressure coupling was done with the Parrinello-Rahman algorithm.

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