Vitaly V. Chaban wrote:
Justin,
Simeone will insert only "the needed number of waters" but not the
full box. :) To do so he will use an option "-maxsol XXX" of genbox.
Indeed, but that's not what you posted in the last message. Just thought I'd
make sure that was clear. I had recommended using -maxsol earlier. In my
experience, it has been easier to insert one component first using -ci -nmol,
then making use of -maxsol.
-Justin
Vitaly
On Mon, Sep 28, 2009 at 5:08 PM, Justin A. Lemkul <[email protected]> wrote:
Vitaly V. Chaban wrote:
Hi Simone,
I would advise you to insert the needed number of waters (genbox -cp
conf.gro -cs water.gro -o conf1.gro) and then do the same with DMSO
((genbox -cp conf1.gro -cs dmso.gro -o conf2.gro). Then just
equilibrate.
I doubt that will work. The first call to genbox there will fill the box
with water, leaving no room for anything else.
-Justin
Vitaly
I need to run a simulation of a protein in a water/DMSO mixture. I can't
quite understand how should I do this... should I normally solvate the
protein with water and then replace a certain number of water molecules
(according to the needed % of DMSO) with DMSO molecules? But in this
case,
how should I do it? Is there a way of replacing solvent molecules with
other
solvent molecules, but of a different type?
I'm sorry but I don't know which procedure to follow.
Thanks in advance
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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