[gmx-users] doubts on running em in vacuo
Kwee Hong
jestan1985 at yahoo.com
Sat Jan 22 11:42:45 CET 2011
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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