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problem in using initram.sh iteratively
- hadiseh
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8 years 10 months ago #4594
by hadiseh
problem in using initram.sh iteratively was created by hadiseh
I want to backmap my system(protein + surfactants) from CG to AA.
I have survived for doing backmapping using ./initram.sh script with GROMACS 4.5.6
However, the problem is that, I want to produce and AA trajectory from my original CG.
1000 .gro files are prepared and I wrote an script for doing this job iteratively.
the problem is that for some frames (.gro files) I received this error several times
step 0Warning: 1-4 interaction between 9370 and 9379 at distance 3.110 which is larger than the 1-4 table size 1.900 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Mostly, it crashes while producing 3-mdpr-0.0002.gro file before going further.
could it be because of number of steps in EM?
The strange thing is that only rerunning the script is enough to achieve a final backmapped file.
I want to automotize this procedure and it is insane to rerun it manually for 1000 time.
if any body knows about this problem I would really appreciate .
by the way, isn't it because of using the improper version of GROMACS?
I have survived for doing backmapping using ./initram.sh script with GROMACS 4.5.6
However, the problem is that, I want to produce and AA trajectory from my original CG.
1000 .gro files are prepared and I wrote an script for doing this job iteratively.
the problem is that for some frames (.gro files) I received this error several times
step 0Warning: 1-4 interaction between 9370 and 9379 at distance 3.110 which is larger than the 1-4 table size 1.900 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Mostly, it crashes while producing 3-mdpr-0.0002.gro file before going further.
could it be because of number of steps in EM?
The strange thing is that only rerunning the script is enough to achieve a final backmapped file.
I want to automotize this procedure and it is insane to rerun it manually for 1000 time.
if any body knows about this problem I would really appreciate .
by the way, isn't it because of using the improper version of GROMACS?
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