[gmx-users] Nvt T-coupling error

[Justin Lemkul]

On 1/6/16 11:07 AM, Poncho Arvayo Zatarain wrote:
>
>
> 	
> 	
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> I`m
> running a simulation of dppe+dppe+ligand+wáter and i`m building
> index with the command gmc make_ndx –f minimiz-gro –o index.ndx.
> When i use the command the following options appears to build the
> index:
> 0
> System    27592 atoms
> 1
> Other      27592 atoms
> 2
> LIG
>                  8 atoms
> 3
> DPPC          8320 atoms
> 4
> DPPE          7744 atoms
> 5
> TIP3          11520 atoms
>
>
>
>
> And
> i selected 3|
> 4 | 2 | 5 and creates the group DPPC_DPPE_LIG_TIP3
> with 27592 atoms. Then i used the command instruction gmx
> grompp -f nvt.mdp -c minimiz.gro -p dppc+dppe+ligand+water.top -n
> index.ndx -o nvt.tpr, i run it and the following error appears:

Well:

> Fatal error: 11520 atoms are not part of any of the T-coupling groups.

This is a clue:

5 TIP3          11520 atoms

and:

tc-grps		= DPPC DPPE    LIG

So there's your problem.

-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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