From: "Michael Shirts" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] confused about rcoulomb<=rlist
Date: Sat, 15 Jul 2006 11:37:52 -0400
For studying effects of cut-off and integration setup on the results
I can see that
Hmm..
Well counting the charged residues leads
to scores of ions, which I think would be a tight squeeze in my water box,
given that each ion should have a hydration shell around it.
I like the idea of neutralizing, then
adding ions to reach a certain ionic strength. However how
Hi,
If you want to add ions near charged residues and
want to know how much, just count the number of charged residues, and
add one positive and one negative charge for the N- and C- termini.
You can use g_sas to locate the solvent-exposed residues if that's
needed.
However, I think that
Hi Guys,
Can anyone tell me how I should go about adding counterions in GROMACS?
Right now I am adding just enough counterions to make the net charge equal
to zero. However I believe I should be adding a counterion for each charged
atom on the surface, according to some algorithm. Is there
I am using the following commandfor solvating my protein but i am stiil getting
my protein at one face of box.
editconf -bt octahedron -f trp2.pdb -o trp2.pdb -c -d 0.6
From: [EMAIL PROTECTED] on behalf of Haberl Florian
Sent: Sun 7/16/2006 6:55 AM
To: Discussi
Hi,
> Hi
> when i am trying to solvate my protein in water box, i am not getting my
> protein in the center of but at one face of water box with some atoms
> outside waterbox. what should i do for this problem? should i move center
> of my protein to the center of water box using some tcl script i
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