[gmx-users] energy minimization error

[James Lord]

Hi Justin,
I have asked this before, but this time I started up from scratch and used
the input files that I know they are fine but again I am getting this
error, Would you please tell me what is wrong in my topology files and
where about in .top files the bond length are defined?

https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing

Cheers
James

On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/16/15 11:35 PM, James Lord wrote:
>
>> Hi Justin
>> Thanks for this. Can you tell me which step(s) this bond length is
>> defined????
>> What should I do (redo) to resolve this issue?
>>
>
> The bonds are defined in the topology.  The DD algorithm reads what's in
> the coordinate file and builds cells based on the geometry it finds there.
>
> Without a full description of what's in your system, what steps you've
> taken to prepare it (full commands, in order), there's little I can suggest
> because it would all be guesswork.
>
>
> -Justin
>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>