On 6/17/13 10:15 AM, 라지브간디 wrote:
Dear gmx users,
I have simulated the heme protein using gromos43a5 ff. I have used virtual
sites2 for the CO ligand and it successfully runs without any error upto
equilibrium state ( em, nvt and npt). However,when i start
running production for 10 ns and it stopped step 17400 and shows few errors:
Please advice me how to avoid this error? How do i link this missing LJ-14 ?
In this context, "missing" interactions simply suggest that your system is
blowing up.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Likely your topology or .mdp settings are wrong.
-Justin
(In here, 1604 and 1605 is C and O of ligand CO)
list of missing interactions:
LJ-14 of 2506 missing 15
Molecule type 'Protein_chain_A'
the first 10 missing interactions, except for exclusions:
LJ-14 atoms 938 1604 global 938 1604
LJ-14 atoms 940 1604 global 940 1604
LJ-14 atoms 942 1605 global 942 1605
LJ-14 atoms 1558 1605 global 1558 1605
LJ-14 atoms 1559 1605 global 1559 1605
LJ-14 atoms 1560 1605 global 1560 1605
LJ-14 atoms 1561 1605 global 1561 1605
LJ-14 atoms 1564 1604 global 1564 1604
LJ-14 atoms 1567 1604 global 1567 1604
LJ-14 atoms 1576 1604 global 1576 1604
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.5.5
Source code file: futil.c, line: 459
File input/output error:
dd_dump_err_0_n10.pdb
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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