[gmx-users] energy minimization error

[Justin Lemkul]

On 6/26/15 7:19 PM, James Lord wrote:
> 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
>

There's nothing I can do with a topology that's a series of #include statements.

Please also remind me what this is all about so I don't have to go digging 
through the archives for something from a month ago.  Lots of things have 
happened since then :)

-Justin

> 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
>>
>> ==================================================
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-- 
==================================================

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

==================================================