Re: vmd-l: problems with CG protein-lipidbilayer-water system

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Mon Nov 23 2009 - 00:51:43 CST

Hi Francesco,

> My first question is: should I downgrade to VMD 1.8.6? Anton's files
> are not that old, 31 AUG 2009.
I've posted the files around that date, but the files themselves are
much older. I haven't been using them for a while :). So, do try
downgrade to VMD 1.8.6. I haven't tried myself (sorry, too busy), but
it may work.

> My second question: are the above files for lipids enough for my task?
I think so.

> My third question: at present is it still advisable to coarse grain
> the components rather that the all-atom final system using the auto cg
> builder?
Yes. It will be faster and you'll have more control with what you are
doing. In principle, it doesn't matter, if you don't mind to wait for
a long time when coarse-graining your whole system, rather than
components (the time it takes for the RBCG tools to coarse-grain a
system grows non-linearly with the number of particles in your system,
N; I think it's N^2 or maybe N^3).

Anton.

On Nov 21, 2009, at 10:00 AM, Francesco Pietra wrote:

> Hi:
> I have already posted fragments in the Subject topic. I got some
> important advice but I am still in the open sea. Therefore, I
> summarize the status, in the hope to get further input. I am aimed at
> setting up a transmembrane protein in a POPC, DOPC (or other common
> polar lipid) bilayer, and water solvated, coarse-grained system. I
> followed Anton's advice (mail archives) to coarse gain separately the
> components rather than the whole system.
>
> I first tried - as an assay - to cg solvate the protein using the
> files that
> Anton has put on the web <http://www.ks.uiuc.edu/Research/CG/rbcg/files/
> >
>
> cgionize.tcl 20-Nov-2009 12:01 8k
> [ ] cgsolvate.tcl 31-Aug-2009 20:19 20k
> [ ] cgwat.pdb 31-Aug-2009 20:19 42k
> [TXT] cgwat.psf 31-Aug-2009 20:19 44k
> [TXT] dopc.cgc 31-Aug-2009 20:19 2k
> [TXT] lipid.cgc 31-Aug-2009 20:19 2k
> [TXT] rbcg-2007.par 31-Aug-2009 20:19 24k
> [TXT] rbcg-2007.top 31-Aug-2009 20:19 8k
>
>
>
> If cgsolvate.tcl is added to
>
> /usr/local/lib/vmd/plugins/noarch/tcl/solvate1.3
>
> it is not seen by the command
>
> package require ...
>
> Then I put cgsolvate.tcl in my working directory. Command
>
> source cgsolvate.tcl
>
> reported
>
> conflicting versions provided for package "solvate": 1.3, then 1.2.
>
>
> My first question is: should I downgrade to VMD 1.8.6? Anton's files
> are not that old, 31 AUG 2009.
>
> My second question: are the above files for lipids enough for my task?
>
> My third question: at present is it still advisable to coarse grain
> the components rather that the all-atom final system using the auto cg
> builder?
>
> Thanks for answering
>
> francesco pietra

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