Re: implementing RBCG

From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Mar 22 2011 - 21:25:54 CDT

Michael,

A first version of Martini is available in the CVS version of NAMD.
The commands are in the userguide available in the CVS, but I'm
copying the Martini section below. Let us know if you have any
problems.

Best,
Chris

5.4 MARTINI Residue-Based Coarse-Grain Forcefield
The MARTINI forcefield for residue-based coarse-grain models allows
simulation of several tens
of atoms as only several large coarse-grained particles [41, 42, 44].
In the MARTINI model, each
protein residue is represented by a backbone bead and usually one or
more sidechain beads.
When preparing MARTINI simulations it is important to include only
those dihedrals specified
by the forcefield. Using the “auto dihedrals” or “regenerate dihedrals”
feature of psfgen will create
dihedrals for all possible sets of four bonded atoms. This is
incorrect for MARTINI and will result
in energy jumps because the dihedral potential function is degenerate
for the angles of 180 degrees
allowed by cosine-based angles.

When using MARTINI the following configuration parameters should be set
as indicated:

cosAngles on
martiniSwitching on
dielectric 15.0
PME off

• cosAngles < enable the MARTINI cosine-based angle potential function >
Acceptable Values: on or off
Default Value: off
Description: Specifies whether or not the MARTINI forcefield is being
used, specifically
cosine-based angle potential function. The cosine-based potential will
only be used for angles
in CHARMM parameter files that specify the cos keyword.

• martiniSwitching < enable the MARTINI Lennard-Jones switching function? >
Acceptable Values: on or off
Default Value: off
Description: Specifies whether or not the MARTINI forcefield is being
used, specifically
the Lennard-Jones switching function.

• martiniDielAllow < Allow dielectrics != 15.0 for use with MARTINI >
Acceptable Values: on or off
Description: off Allows user to specify a dielectric not equal to
15.0, ie a non-standard
dielectric for MARTINI.

On Tue, Mar 22, 2011 at 9:17 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Michael,
> There should no longer be any need for a special version of autopsf; the
> links you posted are to an old stopgap version that fixed a bug (which
> has now been corrected in the main versions).
>
> Could you elaborate on how you tried to build the RBCG models? In order
> to help, we need a concrete series of steps from 1ubq.pdb to your error,
> because when I try doing this it works fine.
>
> Regarding MARTINI, I know a couple of grad students in Klaus's group
> were working on it, but I'm afraid I don't know the current status...
> perhaps a current group member could comment.
>
> Best,
> Peter
>
> On 03/22/2011 04:11 PM, Michael Zimmermann wrote:
>> NAMD Users,
>>
>> I want to do RBCG simulations on some large systems, but have been
>> unable to build RBCG models for small proteins (like 1UBQ) due to
>> "/Error: failed on end of //segment; molecule destroyed./" errors.
>> These are errors for applying the NTER and CTER patches.  If I try to
>> set these to NONE then autopsf also fails.  Following the advice of:
>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/11194.html
>> and
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14725.html
>>
>> I have tried to source a different version of autopsf, but I don't see
>> how to do so.  I have tried to at the tk console, but get: "/conflicting
>> versions provided for package "autopsf": 1.3, then 1.2/"
>>
>> If anyone has further advice on making RBCG models, or a working RBCG
>> model that I could learn from, I would appreciate it.
>>
>> Also, is there any news about using MARTINI in NAMD
>> (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/8802.html)?
>>
>> I am using VMD v.1.9 Windows OpenGL, CUDA on 64-bit WinXP.
>>
>> --
>> Michael Zimmermann
>> Ph.D. student in Bioinformatics and Computational Biology
>> Department of Biochemistry, Biophysics and Molecular Biology
>> Iowa State University
>
>

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char              Fax: 217-244-6078

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