gbis for acetonitrile

Date: Sat Mar 11 2017 - 00:40:15 CST

Hello NAMD,

I have ran the GBIS script for a short peptide considering the environment
to be in aceto-nitrile. for which the "solvent Dielectric" values and
"cut-off" values are altered.
Q1. Now since it just the equilibration and minimization step ,do I need
to run the Dynamics step?

Q2. unlike the explicit system the, Should I consider the setup.psf (the
initial psf, reg and coordinate files) for co-ordinate , structure and
restrain file.

Q3. what periodic cell dimension should i mention. Because, when I have
mentioned the "max + min" xyz co-ordinates attained from gbis.dcd file is
stated to be small in size (Periodic cell has become too small for
original patch grid)

Please provide me an example script (if possible) that has been used for
implicit solvent other than water.

Thanks in anticipation.

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