[gmx-users] work in 4.5.5 but failed in 4.6.1

[Justin Lemkul]

On 8/28/13 1:21 PM, Albert wrote:
> On 08/28/2013 07:07 PM, Justin Lemkul wrote:
>>> WARNING 2 [file helix.itp, line 1]:
>>>    Too few parameters on line (source file toppush.c, line 1501)
>>
>> Looks concerning - what's line 1?
> here is the initial lines:
>
> ; position restraints for part of C-alpha of Protein
>
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     5    1        300        300        300
>    24    1        300        300        300
>
>

Looks normal, so without context of how it is #included, there's not much to 
diagnose here.

>
>>
>>> WARNING 3 [file md.mdp]:
>>>    The sum of the two largest charge group radii (13.715767) is larger than
>>>    rlist (1.000000)
>>>
>>
>> How big is your box?  This may very well be a simple periodicity issue.
>>
>> http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
>>
>>
>> -Justin
>
> I've see this informations from gromacs website. my box is:
>
>     6.96418   6.96418   9.77176
>
> in the last line of my input .gro file.
>
> I don't understand, why this warning not appear in 4.6.3, but failed in 4.5.5....
>

The misinterpretation of periodicity in warning 3 was a bug that was fixed at 
some point, so the fact that it doesn't show up in 4.6.3 makes sense.

-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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