[gmx-users] work in 4.5.5 but failed in 4.6.1
jalemkul at vt.edu
Wed Aug 28 19:25:02 CEST 2013
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
>>> 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.
> 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 A. Lemkul, Ph.D.
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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