Tree wrote:
Dear Justin and Mark:
Thank you for your reply.
Okay, regarding the 'entanglement' of a polymer, I can ask in a
different way, maybe.
In a protein simulation, I've seen the motion of 'one' protein
macromolecule such as a sort of vibrating, folding, moving around, or
changing its shape (becoming thinner, thicker, spherical, or column,
etc...).
What you observe will also be highly dependent upon the protein itself. Whereas
a stable, well-folded protein may not do much over time, different proteins may
be more dynamic (those that are intrinsically unstructured or unstable).
Just because a protein acts a certain way, does *not* mean that all simulation
results will be comparable. The choice of .mdp parameters will play a role as well.
I understand that is originated from potentials defined as 'bond
(stretch)', 'angle', 'dihedrals' and 'improper dihedrals', which are
different from metal simulation.
Not entirely. The force field functional form also includes nonbonded terms
(L-J and Coulombic interactions) that will play a role in dynamics. Hence why
using cut-off for electrostatics is a bad choice, since you will get artefacts.
So, my questions is whether "this understanding" is correct or not...
If not, I hope to learn how those potentials work for the one
macromolecule.
Since I can a result anyway, I thought it was okay... :)
Right, I've changed the cutoff range with a artificial (and arbitrary)
guess...
The correct approach is to never be arbitrary. Read the primary literature for
that particular force field and how it was derived. Read about how people use
the force field and whether or not modifications to the original derivation are
also accurate.
-Justin
As suggested by Justin, I will change mdp file and increase the time
duration.
If I get a good(?) result, I will post-!
Thank you so much.
Sincerely yours,
Chansoo
On Sat, Mar 7, 2009 at 5:45 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Mark Abraham wrote:
----- Original Message -----
From: Tree <[email protected] <mailto:[email protected]>>
Date: Sunday, March 8, 2009 6:35
Subject: Re: [gmx-users] Polymer entanglement simulation
To: [email protected] <mailto:[email protected]>, Discussion list
for GROMACS users <[email protected]
<mailto:[email protected]>>
Dear Justin and Users:
Thank you for your fast reply.> First, I want to clarify the
"entanglement", so I can get more accurate consult from you! :)
Of course, the non-bonded interaction makes entanglement
"among" polymer chains.> However, "Entanglement" here means
the "intra"chain (intramolecular) one.
In other words, one chain polymer (having enough monomers
inside, e.g. 1 chain polymer containing 20 monomers) can be
entangled with itself. > This is the reason that I gave
force filed parameters related to the bond (stretch), angle,
dihedral, and improper dihedral.
I don't understand what you mean by "entanglement", nor what
this has to do with your force field parameters.
This is also reason that I have suspected the topology file,
which assign force field...> In addition, I am putting my
setting here.>
tc-grps = carbon hydrogen
This is a train wreck waiting to happen. Please consider doing
some more background reading and/or tutorial material :-)
As is using cut-off for electrostatics, with the bizarre cutoff's
you've defined (rlist, rcoulomb, rvdw). Use PME with at least a
1.0-nm cutoff for all three and see if you get better results.
Furthermore, as I said before, timeframe might be an issue. 1 ns is
not nearly long enough to see such behavior. Try tens of
nanoseconds, if not more.
-Justin
Mark
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
