On Aug 16, 2010, at 1:33 PM, Anirban Ghosh wrote:
Thanks a lot XAvier for clarifying my doubt. You mean to say "-rdd"
option with mdrun, right?
yes
And why does this curvature of the membrane occurs?
No idea!
Thanks a lot once again.
Regards,
Anirban
On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole <x.peri...@rug.nl>
wrote:
Although a bit worrying the curvature of your bilayer is not
responsible for the error message you are seeing.
to solve the problem you have to increase to use the -rrd option
(see manual for explanation). Typicaly a value of 1.4 to 1.6 should
be fine.
On Aug 16, 2010, at 12:16 PM, 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.
Regards,
Anirban
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