Sai Pooja wrote:
The pull tutorial uses npt simulations.. is that required by the
algorithm or can one use nvt after the system has been sufficiently
equilibrated using npt?
Use whatever conditions are appropriate for your system. Tutorials should not
be viewed as the only applicable conditions, merely one such example of what
might be done.
-Justin
On Fri, Apr 1, 2011 at 7:32 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to
create a merged [moleculetype] to apply distance restraints. If
you're just trying to use a harmonic potential to define some
sampling distance (for US), then distance restraints are not
necessary, just apply the pull code.
-Justin
Sai Pooja wrote:
Also, the chains do not diffuse apart in time since they are
position restrained(some parts of each chain are ...)
On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja <saipo...@gmail.com
<mailto:saipo...@gmail.com> <mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>>> wrote:
Hi,
I have 5 chains in my Protein. I want to apply distance
restraints
for doing Umbrella Sampling for 2 atoms on different chains. Is
there a way to do this since the two chains have separater
itp files.
Pooja
-- Quaerendo Invenietis-Seek and you shall discover.
--
Quaerendo Invenietis-Seek and you shall discover.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
Quaerendo Invenietis-Seek and you shall discover.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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