From NWChem
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| 7:44:55 PM PDT - Thu, Mar 14th 2013 |
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Hi,everyone...
I'm trying to run a free energy calculation on a solvated system with 59 atoms in the QM region, it stopped for the problem:
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* 0: Deviation too large for solvent 15
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Last System Error Message from Task 0:: Inappropriate ioctl for device
[0] MPI Abort by user Aborting program !
0:0::: 15
(rank:0 hostname:node2 pid:11364):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/armci.c:ARMCI_Error():208 cond:0
[0] Aborting program!
p0_11364: p4_error: : 15
It seems that this happens for the wrong solvent configuration, I just don't know how to solve the problem, Could you give me some suggestions ?
Thanks,
--dandelion
My input file:
start abc
md
system abc_neb
equil 5000
cutoff 1.5 qmmm 1.5
noshake solute
isotherm
end
qmmm
print low
nsamples 5000
ncycles 2
end
set qmmm:fep_geom abc_start.xyzi abc_end.xyzi
set qmmm:fep_esp abc_start.esp abc_end.esp
set qmmm:fep_lambda 0.0 0.1
set qmmm:fep_deriv .true.
task qmmm dft fep
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| 3:43:53 PM PDT - Tue, Mar 26th 2013 |
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| More often than not this is caused by a simulation box that is too tight. Try recreating the restart file with a larger envelope, or edit the restart file and increase the box dimensions.
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| 5:29:03 AM PDT - Wed, Mar 27th 2013 |
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Quote:Tps Mar 26th 10:43 pmMore often than not this is caused by a simulation box that is too tight. Try recreating the restart file with a larger envelope, or edit the restart file and increase the box dimensions.
OK, thank you very much. I will have a try.
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| 6:49:20 PM PDT - Thu, Oct 24th 2013 |
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Quote:Tps Mar 26th 10:43 pmMore often than not this is caused by a simulation box that is too tight. Try recreating the restart file with a larger envelope, or edit the restart file and increase the box dimensions.
I have a similar problem. My job could run for a certain no. of cycles and then aborted. Your suggestion means we need to start the calculation form the beginning by recreate a new restart file? Does this 'envelope' keyword work only along with 'solvate' keyword? Can I use it with a structure which already has solvent?
For editing the restart file, how much should we increase the dimension box?
I have seen similar problem for NEB calculation in this thread http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id300/%22Deviation_too_large_for_so... and Marat suggested to run constant energy MD for few steps. I've tried but also got the same error. I also examined the structure and haven't seen any overlapping or bad contacts between solvent and the solute.
Best,
Tee
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Edited On 6:54:52 PM PDT - Thu, Oct 24th 2013 by Tpirojsi
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| 1:51:20 AM PST - Tue, Nov 26th 2013 |
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how to solve this problem?
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Quote:Tps Mar 26th 10:43 pmMore often than not this is caused by a simulation box that is too tight. Try recreating the restart file with a larger envelope, or edit the restart file and increase the box dimensions.
Dear everyone,
I just want to know how to solve the problem of "Deviation too large for solvent" problem. If you can provide me some suggestions, I am very appreciated.
Based on my experience, it is a very common error in NWChem computation. The possible reason is if one solvent deviate too large and move out of the box, then it should change its coordinates according to periodic condition. Am I right?
In order to solve this problem Tps propose that we can edit the restart file and increase the box dimensions. So the question is how long we can increase? In my simulation, I change the box dimension from 8 angstrom to 8.3, but still error.
Thanks for your time.
Best,
Jingbo
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