Thanks a lot XAvier for clarifying my doubt. You mean to say "-rdd" option with mdrun, right? And why does this curvature of the membrane occurs?
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 >> <sim.jpeg>-- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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