[gmx-users] Constraints errors

[Justin Lemkul]

On 1/20/16 11:16 PM, Alireza Moradzadeh wrote:
> Dear Users,
> I want to simulate [BMIM][PF6] using following itp
> [ moleculetype ]
> PF6 2
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> 1 P 1 PF6 P1 1 1.13 30.974
> 2 FP 1 PF6 F2 2 -0.33 18.998
> 3 FP 1 PF6 F3 3 -0.33 18.998
> 4 FP 1 PF6 F4 4 -0.33 18.998
> 5 FP 1 PF6 F5 5 -0.33 18.998
> 6 FP 1 PF6 F6 6 -0.33 18.998
> 7 FP 1 PF6 F7 7 -0.33 18.998
> [ bonds ]
> 1 2 1
> 1 3 1
> 1 4 1
> 1 5 1
> 1 6 1
> 1 7 1
> [ angles ]
> 2 1 3 1
> 2 1 4 1
> 2 1 6 1
> 2 1 7 1
> 3 1 4 1
> 3 1 5 1
> 3 1 7 1
> 4 1 5 1
> 4 1 6 1
> 5 1 6 1
> 5 1 7 1
> 6 1 7 1
> 2 1 5 1 180. 1165.
> 3 1 6 1 180. 1165.
> 4 1 7 1 180. 1165.
>
> But I get following errors for both of my molecules.
>
> Molecule type "PF" has 21 constraints.
> For stability and efficiency reasons there should not be more constraints
> more than internal degree of freedoms: 15
> Is it right to use maxwarn in this case?!
>

You're being told that what you're trying to do (presumably via constraints = 
all-angles) is not physically stable.  You can override this, of course, but 
then don't come asking for help when your simulation crashes.  grompp already 
warned you :)

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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