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
--
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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