[gmx-users] exclusions

[Steven Neumann]

I used bonds but with [ exclusions ] of 2516 atoms:
1 2 3..... 2516
2 3 4 .....2516
...
2515 2516

when grompp I get an error:

"An input file contains a line longer than 4095 characters". It does indeed
contains over 4095 as its 11470. Do you know how to overcome this?

Steven



On Thu, Dec 5, 2013 at 7:25 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Thank you!
>
> Steven
>
>
> On Thu, Dec 5, 2013 at 6:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 12/5/13 12:57 PM, Steven Neumann wrote:
>>
>>> Thanks, I will apply harmonic bonds with whatever force constant then.
>>> Would that speed up the performance with all exclusions and bonds?
>>>
>>
>> Exclusions would make a big difference.  Bonds will not produce any
>> noticeable change.
>>
>>
>>  Does the increase of the force constant in posre.itp make the simulation
>>> slower? I used Fx=Fy=Fz=30 000
>>>
>>>
>> No.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==================================================
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>