[gmx-users] Grompp error

[Justin Lemkul]

On 5/30/16 10:40 AM, Anurag Dobhal wrote:
> Dear Gromacs users
>
> I am solvating my molecule ( a ploymer chain, having 78 atoms) in Propan-2-one
> [ molecules] = acetone. I have already updated  [ molecules ] section in
> the topology file (topol.top) after the solvation step.
>
> after the sucessful energy minimization step, while runing grompp I am
> geting an error,
>
> " Excluding 3 bonded neighbours molecule type 'Other'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'acetone'
> turning all bonds into constraints...
> Setting gen_seed to 3080450167
> Velocities were taken from a Maxwell distribution at 300 K
> Removing all charge groups because cutoff-scheme=Verlet
>
> Fatal error:
> Atom 79 in multiple T-Coupling groups (1 and 2) "
>
> The error means that T-coupling is treating both the polymer (other) and
> solvent (acetone) as other molecules.
> How can I rectify the error ?
>

You haven't shown us what you've set as tc-grps but there is clearly redundancy 
between whatever those groups are.  If you have multiple groups, you need to 
ensure that they are defined correctly, using index groups as needed.

-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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