[gmx-users] list of missing LJ-14 interactions:

[Justin Lemkul]

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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