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NVT & NPT run for coarse grained simulation
- xudongh
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I'm trying to run a NVT and NPT equilibration on this CG model following the Protein In Water tutorial. Is there a supplied NVT.mdp or NPT.mdp file for this type of CG system? I adapted another source's nvt and npt.mdp file, and I tried to run it, i get the following error:
Fatal error:
There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 5.2375 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
I don't think I can change the node because that was decided way earlier on in the run many steps before, and I would imagine if I change the node, i change the entire structural property.
Any suggestions? Let me know.
**Is it because we coarse grained it, which leaves it not enough atoms?
Thanks :)
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- xavier
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try to add the "-pd" (particle decomposition) option to mdrun ... should fix it
xudongh wrote: Hello all,
I'm trying to run a NVT and NPT equilibration on this CG model following the Protein In Water tutorial. Is there a supplied NVT.mdp or NPT.mdp file for this type of CG system? I adapted another source's nvt and npt.mdp file, and I tried to run it, i get the following error:
Fatal error:
There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 5.2375 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
I don't think I can change the node because that was decided way earlier on in the run many steps before, and I would imagine if I change the node, i change the entire structural property.
Any suggestions? Let me know.
**Is it because we coarse grained it, which leaves it not enough atoms?
Thanks :)
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- xudongh
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When i try -pd in my mdrun, the run doesn't last for 5000 steps, infact it ends after step 0. Is it because the system is too small for a 5000 step run?
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- xavier
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xudongh wrote: @ xavier,
When i try -pd in my mdrun, the run doesn't last for 5000 steps, infact it ends after step 0. Is it because the system is too small for a 5000 step run?
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- xudongh
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xavier wrote: No, then you have another problem! Try to identify it!
xudongh wrote: @ xavier,
When i try -pd in my mdrun, the run doesn't last for 5000 steps, infact it ends after step 0. Is it because the system is too small for a 5000 step run?
Oh crap. That reminds me when I ran the em.mdp (energy minimization of the solvated structure) it was also set to 5000 steps, it did run all 5000 steps, but the run was rather quick compared to all atom based system. Was that a hallmark feature of coarse grained the structure so it cuts down computational time or did I mess up there too?
Thanks,
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- xavier
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xudongh wrote:
xavier wrote: No, then you have another problem! Try to identify it!
xudongh wrote: @ xavier,
When i try -pd in my mdrun, the run doesn't last for 5000 steps, infact it ends after step 0. Is it because the system is too small for a 5000 step run?
Oh crap. That reminds me when I ran the em.mdp (energy minimization of the solvated structure) it was also set to 5000 steps, it did run all 5000 steps, but the run was rather quick compared to all atom based system. Was that a hallmark feature of coarse grained the structure so it cuts down computational time or did I mess up there too?
Thanks,
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- xudongh
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xavier wrote: !? Yes CG simulations cut down in computational time ...
xudongh wrote:
xavier wrote: No, then you have another problem! Try to identify it!
xudongh wrote: @ xavier,
When i try -pd in my mdrun, the run doesn't last for 5000 steps, infact it ends after step 0. Is it because the system is too small for a 5000 step run?
Oh crap. That reminds me when I ran the em.mdp (energy minimization of the solvated structure) it was also set to 5000 steps, it did run all 5000 steps, but the run was rather quick compared to all atom based system. Was that a hallmark feature of coarse grained the structure so it cuts down computational time or did I mess up there too?
Thanks,
@Xavier.
For a MD.mdp run, is 5 million step on a cg system too much and redundant?
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- djurre
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- riccardo
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www.gromacs.org/Documentation/Errors#The...ze_or_decrease_rlist
Something is going very wrong - aka, your system is exploding or similar. Note that you cannot decrease rlist at will. This is a parameter which goes into the parametrization of a force field, thus it is usually fixed to the value which has been used to parametrize the force field. If you change it, who knows in which way you'll change the behavior of the force field.
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- riccardo
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