[gmx-users] energy minimization error

[James Lord]

Hi Justin
For now I  used


*mdrun -nt 1*


* and got rid of this error so hopefully the simulation wont crash. *

*Cheers*

*James*


On Sat, Jun 27, 2015 at 11:19 AM, James Lord <jjamesgreen110 at gmail.com>
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
>
> 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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>
>