[gmx-users] problem of GLUP

[Justin Lemkul]

On 1/21/14, 6:55 AM, Albert wrote:
> Hello:
>
> I've got a protonated GLUP in the protein. I try to run command:
>
> grompp_mpi -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -n
>
> it always claimed 16 atoms doesn't belongs to any 16 atoms are not part of any
> of the T-Coupling groups
>
> I make a new index file by make_ndx like:
>
>  > 1|13
>
> Copied index group 1 'Protein'
> Copied index group 13 'GLUP'
> Merged two groups with OR: 4960 16 -> 4976
>
>   28 Protein_GLUP        :  4976 atoms
>
>
> This error is no longer there.
>

Consider step #5:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

> However, I noticed that the speed of my MD simulations become unbilevable slow
> with command in a cluster:
>
> mpirun -np 144 mdrun_mpi -v -s nvt.tpr -c nvt.gro -g nvt.log -x nvt.xtc
>
>   I don't know whether because of this issue. Here is my nvt.mdp settings:
>

Seriously doubtful.  Check the health of the nodes on which the job is running.

-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
20 Penn St.
Baltimore, MD 21201

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

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