Hello Krisztina,
I did an atomistic simulation on a isotactic and atatic poly(methyl methacrylate) (PMMA) melt using Amber (DOI:10.1080/08927020903536374). The force field used in the study was a simple extension of Glycam06. While intended for carbohydrates modeling, Glycam06 was originally developed and optimized using simple organic compounds and is fairly transferable. This extension was the foundation for developing a larger force field for modeling lipopolysaccharide membranes (DOI: 10.1021/ct300534j).
However, atomistic simulation of polymer melts is not the best way to study these systems, as I have learned. The problem is in getting conformational sampling and the long simulation time needed due to long auto-correlation times. There are methods to get around this, including forward and back mapping between atomistic and coarse-grained models. Many of the polymer simulations are done at the mesoscale using coarse-grained models.
When I was learning about this area, I found the research by Drs. Kurt Kremer and Florian Mueller-Plate to be enlightening. If you are interested in this area take a look at the articles and research groups I give below - they should get you started on uncovering more polymer modeling literature.
Best regards,
Karl
Title: Novel Simulation Approaches for Polymeric and Soft Matter Systems
Author(s): Cerda, Joan J.; Holm, Christian; Kremer, Kurt
Source: MACROMOLECULAR THEORY AND SIMULATIONS Volume: 20 Issue: 7 Special Issue: SI Pages: 444-445
Title: Temperature and Pressure Dependence of Polystyrene Dynamics through Molecular Dynamics Simulations and Experiments
Author(s): Harmandaris, Vagelis A.; Floudas, George; Kremer, Kurt
Source: Macromolecules Volume: 44 Issue: 2 Pages: 393-402 Published: JAN 25 2011
Title: Fine-graining without coarse-graining: an easy and fast way to equilibrate dense polymer melts
Author(s): CARBONE, P; KARIMI-VARZANEH, HA; MULLER-PLATHE, F Source: FARADAY DISCUSSIONS Volume: 144 Pages: 25-42 Published: 2010
Title: Molecular dynamics simulations of polyaminoamide (PAMAM) dendrimer aggregates: molecular shape, hydrogen bonds and local dynamics
Author(s): CARBONE, P; MULLER-PLATHE, F Source: SOFT MATTER Volume: 5 Issue: 13 Pages: 2638-2647 Published: 2009
Apel, U. M.; Hentschke, R. & Helfrich, J. Molecular Dynamics Simulation of Syndio- and Isotactic Poly(methyl methacrylate) in Benzene Macromolecules, 1995, 28, 1778-1785
Ghanbari, A.; Boehm, M.C.; Mueller-Plathe, F. A Simple Reverse Mapping Procedure for Coarse-Grained Polymer Models with Rigid Side Groups
Macromolecules 2011, 44, 5520-5526
Depa, P. K. & Maranas, J. K. Speed up of dynamic observables in coarse-grained molecular-dynamics simulations of unentangled polymers JOURNAL OF CHEMICAL PHYSICS, 2005, 123
Izvekov, S. & Voth, G. A. Modeling real dynamics in the coarse-grained representation of condensed phase systems JOURNAL OF CHEMICAL PHYSICS, 2006, 125
Okada, O.; Oka, K.; Kuwajima, S. & Tanabe, K. Molecular dynamics studies of amorphous poly(tetrafluoroethylene) MOLECULAR SIMULATION, 1999, 21, 325-342
Paul, W. & Smith, G. D. Structure and dynamics of amorphous polymers: computer simulations compared to experiment and theory REPORTS ON PROGRESS IN PHYSICS, 2004, 67, 1117-1185
Wu, C. & Xu, W. Atomistic molecular modelling of crosslinked epoxy resin Polymer, 2006, 47, 6004-6009
Wunderle, B.; Dermitzaki, E.; Hoelck, O.; Bauer, J.; Walter, H.; Shaik, Q.; Raetzke, K.; Faupel, F.; Michel, B. & Reichl, H. Molecular dynamics approach to structure-property correlation in epoxy resins for thermo-mechanical lifetime modeling Microelectronics Reliability, 2010, 50, IEEE CPMT; Nokia; NXP Semiconductors; Robert Bosch GmbH; Siemens
Yarovsky, I. & Evans, E. Computer simulation of structure and properties of crosslinked polymers: application to epoxy resins Polymer, 2002, 43, 963-969
----- Original Message -----
From: "Krisztina Feher" <feher_krisztina.yahoo.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Sunday, July 14, 2013 9:50:17 AM
Subject: Re: [AMBER] Residue chirality
Hi Karl,
Sorry for the diversion of the topic, but I got curious: did you use AMBER for an organic polymer? With which forcefield? Do you know any description of such simualtions in the literature? (I did some searches, but so far did not find any...)
regards,
Krisztina
--------------------------------------------
On Tue, 7/9/13, Karl N. Kirschner <kkirsch.scai.fraunhofer.de> wrote:
Subject: Re: [AMBER] Residue chirality
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Tuesday, July 9, 2013, 5:27 PM
Hi Carlos and Jason,
I ran into this problem when I was working on a model
for creating a short strand of PMMA polymer several years
ago. (Granted, not something that Amber was originally
created to handle.) Since these residues were nonstandard, I
built my own prep files and linked them together in xleap
using the sequence command, as one would do for a peptide.
When I measure the prep file's improper torsion angle
around the chiral center using the measureGeom command, for
one residue (PMD) I obtain a value of +119.5, and for the
other (PML) I obtain -119.5.
When I do the same measurement, but now one the short
"polymer" (BEG-PML-PMD-END), I obtain values of -118.5 (PML)
and -118.5 (PMD).
Unless I am missing something, this shows that PMD
had its chirality altered by xleap. Granted, that I may have
introduced an error into the prep files, but I have triple
checked them. Also note that if I were to save the
BEG-PML-PMD-END as a pdb file, and opened it up in an
external viewer, there are incorrect bonds added to the
molecule due to inappropriate short distances-- so I know
that the prep files are not conformationally optimized for
the sequence command. Not really knowing the leap code, I
still didn't expect the change in chirality.
All of this was done using: "Latest patch applied to
AmberTools12: 31". The leap input and part of the log file
are included below. If you see something obvious in my
thoughts or the leap input, I would appreciate hearing it.
(I personally do not need this example to be solved, and I
use it only for demonstrating what I encountered before.)
Bests,
Karl
leap input:
-----------
logfile leap.log
source leaprc.ff99SB
loadAmberPrep BEG.prep
loadAmberPrep PML.prep
loadAmberPrep PMD.prep
loadAmberPrep END.prep
poly = sequence {BEG PML PMD END}
measureGeom PML.1.C4 PML.1.C5 PML.1.C3 PML.1.C2
measureGeom PMD.1.C4 PMD.1.C5 PMD.1.C3 PMD.1.C2
measureGeom poly.2.C4 poly.2.C5 poly.2.C3 poly.2.C2
measureGeom poly.3.C4 poly.3.C5 poly.3.C3 poly.3.C2
leap.log:
---------
> measureGeom PML.1.C4 PML.1.C5 PML.1.C3 PML.1.C2
Torsion angle: -119.48 degrees
> measureGeom PMD.1.C4 PMD.1.C5 PMD.1.C3 PMD.1.C2
Torsion angle: 119.50 degrees
> measureGeom poly.2.C4 poly.2.C5 poly.2.C3 poly.2.C2
Torsion angle: -118.47 degrees
> measureGeom poly.3.C4 poly.3.C5 poly.3.C3 poly.3.C2
Torsion angle: -118.47 degrees
----- Original Message -----
From: "Carlos Simmerling" <carlos.simmerling.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Tuesday, July 9, 2013 2:06:05 PM
Subject: Re: [AMBER] Residue chirality
I've done this in tleap many times and it does work. The
issue here is
probably in the details. What was the old a new sidechain?
What is nearby?
When leap built it, did it fit without clash? Was the
chivalry wrong coming
from leap, or after some minimization?
Note that leap can do this, but it won't try to optimize the
location. In
most cases you probably want to use a different program to
build initial
structures, not leap. Swisspdb does a reasonable job of
sidechain
placement.
On Jul 9, 2013 5:25 AM, "Karl N. Kirschner" <kkirsch.scai.fraunhofer.de>
wrote:
> Hi,
>
> At one time there was a bug concerning
this in tleap (and g/sleap??),
> and I am not sure if it was ever corrected. If I recall
correctly, the only
> work-around I found was to construct the enantiomer
using an external
> editor (e.g. PyMol) and load it into xleap. This
preserved the connectivity
> and dihedral angles.
>
> Cheers,
> Karl
>
> ----- Original Message -----
> From: tdo.chem.ucsb.edu
> To: amber.ambermd.org
> Sent: Tuesday, July 9, 2013 11:07:58 AM
> Subject: [AMBER] Residue chirality
>
> Hello,
>
> I try to perform mutations on a peptide by removing the
sidechain atoms
> and replacing the old residue names with new residue
names, then letting
> tleap add in the missing atoms. I check the chirality
of the residues and
> find out that I don't have the correct chirality (i.e.,
I compute the
> chirality dihedral angles and obtain both positive and
negative numbers).
>
> Is there any better way to do mutations with
Amber/tleap? How can I fix
> the incorrect chirality?
>
> Thank you,
>
>
>
>
>
>
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>
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>
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Received on Mon Jul 15 2013 - 02:30:03 PDT
