Anirban Ghosh wrote:
Hi ALL,
I have made a CGMD system with multiple copies of a single protein in
bilayer, by replicating the monomer using genconf in the X-Y plane.
After running CGMD for about 100 ns, I am getting the following error:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Energies (kJ/mol)
Bond G96Angle Proper Dih. Improper Dih. LJ (SR)
4.73694e+04 3.00928e+04 4.68451e+03 8.26028e+02 -1.29727e+06
Coulomb (SR) Potential Kinetic En. Total Energy Temperature
-7.97216e+03 -1.22227e+06 2.24656e+05 -9.97613e+05 3.21675e+02
Pressure (bar) Cons. rmsd ()
-9.97540e+00 1.69233e-05
Not all bonded interactions have been properly assigned to the domain
decomposition cells
A list of missing interactions:
G96Angle of 28064 missing 1
Molecule type 'DSPC'
the first 10 missing interactions, except for exclusions:
G96Angle atoms 10 11 12 global 5309 5310 5311
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.7
Source code file: domdec_top.c, line: 341
Fatal error:
1 of the 62352 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
On visual inspection I found that the bilayer is becoming curved (image
attached). In the .top file I have mentioned the different monomers of
my system as:
--------------------------------------------------------------------------------------------------------------
[ system ]
PROT in DSPC Bilayer
[ molecules ]
Protein 1
DSPC 104
W 1397
NA+ 0
CL- 4
Protein 1
DSPC 104
W 1397
NA+ 0
CL- 4
-------------------------------------------------------------------------------------------------------------
How can I resolve this error? Any suggestion is welcome.
Search the list archive. This error has come up before, and I know there's been
at least one instance of it for a CG system. I believe the answer was to
increase -rdd (since bonded interactions occur at longer distance in CG
systems), but please do the search for yourself.
-Justin
Regards,
Anirban
------------------------------------------------------------------------
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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