[gmx-users] long-stick molecule solvation

[Justin Lemkul]

On 11/4/15 9:22 AM, xy21hb wrote:
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> Dear Justin,
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> Below are the commands I used with all the files attached.
>   https://drive.google.com/file/d/0B4Quti6TfNU_djIwYUZvX3U5NHc/view?usp=sharing
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>   pdb2gmx -f 4KE2.pdb -missing -ignh -o double

Never use -missing.

>   gmx editconf -f double.gro -o d-box -c -d 0.5 -bt triclinic -princ
>   gmx solvate -cp d-box.gro -cs spc216.gro -o d-solv.gro -p topol.top
>   grompp -f em.mdp -c d-solv.gro -p topol.top -o em
>   mdrun -v -s em
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If you visualize d-solv.gro you will see that you have ridiculous coordinates 
for HB atoms in the 0MET residue; this is the cause of your problem, and mdrun 
points you to this fact directly:

WARNING: Listed nonbonded interaction between particles 1 and 8
at distance 6.219 which is larger than the table limit 2.000 nm.

Atom 1 is the N-terminal N, and atom 8 is HB1.

Note also that you have made your box fit very tightly to your protein, and any 
small amount of rotation will lead to unphysical interactions and minimum image 
violations.

-Justin

-- 
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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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