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
em_steep.mdp
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