[gmx-users] doubts on running em in vacuo

[Kwee Hong]

Hi

In John's "GROMACS tutorial for solvation study of spider toxin peptide", he has 
included a suggested em.mdp files to set up an in vacuo minimization.
But I had some noted while conducting the grompp before em.

Analysing residue names:
There are:    35    Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 990.00
Largest charge group radii for Van der Waals: 0.238, 0.238 nm
Largest charge group radii for Coulomb:       0.238, 0.238 nm

NOTE 2 [file em_steep.mdp]:
  The sum of the two largest charge group radii (0.476006) is larger than
  rlist (1.400000) - rvdw (1.000000)



NOTE 3 [file em_steep.mdp]:
  The sum of the two largest charge group radii (0.476006) is larger than
  rlist (1.400000) - rcoulomb (1.000000)


This run will generate roughly 0 Mb of data

There were 3 notes

Back Off! I just backed up em.tpr to ./#em.tpr.1#

gcq#243: "Uh-oh .... Right Again" (Laurie Anderson)

I've read through some of the posts in the mailing list and realised that doing 
some adjustment on the cut-off would solve this. Yet I'm not sure how to justify 
the adjustment.

Option A: Increase my rlist to 1.5 leaving the rest cut-off at 1.0? And set my 
rcoulomb_switch and rvdw_swithch at 0.8?
Option B: Increase my rlist to 1.6 while leaving the rest cut-off at 1.2 and set 
my rcoulomb_switch and rvdw_swithch at 1.0?

I'm using GROMACS-4.5.3. And I attach mt em_steep.mdp file i this email.
Suggestions are all welcomed.

Thanks,
Joyce

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