make_ndx -f conf.gro -o my.ndx
'SOL'
'SHL'
q
(you need to put the single quotes)
in your .mdp add:
freezegrps = SOL
freezedim = Y Y Y
energygrp_excl = SOL SOL
energygrps = SOL SHL Protein
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What procedure will be better? Freeze or position restrain?
Anthony
On Monday 01 May 2006 7:17 am, Anthony Cruz wrote:
> On Friday 28 April 2006 12:02 pm, David van der Spoel wrote:
> > Anthony Cruz wrote:
> > > Hi:
> > > I want to make a simulation of a small pepetide in a box of water but I
> >
On Friday 28 April 2006 12:02 pm, David van der Spoel wrote:
> Anthony Cruz wrote:
> > Hi:
> > I want to make a simulation of a small pepetide in a box of water but I
> > want to freeze or restrain the movement of all water molecules that have
> > a distance grater that 3 A from the protein surface
Anthony Cruz wrote:
Hi:
I want to make a simulation of a small pepetide in a box of water but I want
to freeze or restrain the movement of all water molecules that have a
distance grater that 3 A from the protein surface. Right know the water that
are within 3 A of the protein, have a differe
Hi:
I want to make a simulation of a small pepetide in a box of water but I want
to freeze or restrain the movement of all water molecules that have a
distance grater that 3 A from the protein surface. Right know the water that
are within 3 A of the protein, have a different residue name (SHL)
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