[gmx-users] Error in mdrun

[Justin Lemkul]

On 10/21/16 1:54 PM, Harimuthu wrote:
> hello sir
>
> While running the protein in water energy minimisation
> gmx mdrun -v -deffnm em
> an error is occurred as follows
>
> Program gmx mdrun, VERSION 5.1.2
> Source code file:
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555
>
> Fatal error:
>
> step 14: Water molecule starting at atom 8686 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>

Have you visited this site and the linked pages?  Everything about 
troubleshooting generic failures is laid out completely on the GROMACS website, 
and the many thousands of posts in the archive that have deal with the same 
exact error.

-Justin

>
> in that i searched the error in input file which was in 8686 atom and found
> a error in coordinate value of water it was as
> ATOM   8686  OW  SOL  1551       0.823  30.858  10.228  1.00
> 0.00
> ATOM   8687  HW1 SOL  1551       0.825  31.173  11.177  1.00
> 0.00
> ATOM   8688  HW2 SOL  1551      95.631  30.777   9.906  1.00  0.00
>
> in this the third atom X coordinate is 95.631 and i changed it into 0.631 i
> dont know whether to relible or no, if i do potential graph it is good to
> see, so can anyone help me in solving this problem
> With regards
> Harimuthu
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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