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

[Justin Lemkul]

On 8/28/13 11:48 AM, Albert wrote:
> Hello:
>
> I am constraining one part of the protein and trying to generate md.tpr with
> command:
>
> grompp -f md.mdp -c npt4.gro -n -o md.tpr
>
> it works fine in 4.6.3, but it failed in 4.5.5 with following warning messages:
>
>
> WARNING 1 [file md.mdp, line 65]:
>    Unknown left-hand 'cutoff-scheme' in parameter file

Makes sense; this option did not exist before version 4.6.

> WARNING 2 [file helix.itp, line 1]:
>    Too few parameters on line (source file toppush.c, line 1501)

Looks concerning - what's line 1?

> 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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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