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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Nov 22 2009 - 15:32:18 CST

Hello Axel:
When I don't know the answer, or I don't want letting it know, I stop
cheating or writing. Frankly, knowing that you have developed a secret
philosopher stone is not what users of these two software suites are
interested in.

Hope those who know will help.

Cheers and good night (or good day, it depends on where you are based).

francesco

On Sun, Nov 22, 2009 at 9:41 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Sun, Nov 22, 2009 at 2:17 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>> Hello Axel:
>> Thanks for the clarifications. If you have direct experience with,
>> could you please list the files needed by vmd1.8.7 in order to build
>
> why do you keep asking this? it is so simple to find it out by just trying...
>
>> the separate components of a system composed of
>
> no, i don't use this kind of coarse graining. our group has been working
> on a different, much more specific and accurate model, which has been
> implemented into LAMMPS and HOOMD. i would have recommended
> using it, but the lipid parametrizations have not yet been published.
>
>> protein+lipid_bilayer+solvation_water? No problems for the protein in
>> vacuo with the latest autopsf.tcl provided by Peter Freddolino (recent
>> vmd archives). Of course I am not expecting to just press a button,
>> that is, I am prepared to work also outside CG Builder.
>>
>> I was mislead by the date of cgsolvate.tcl because I use to put "-p"
>> when I make copies of files; a way to keep things in order.
>
> never assume that everybody does things the same way that you do it.
>
> axel.
>
>>
>> Thanks
>> francesco
>>
>> On Sat, Nov 21, 2009 at 11:54 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>> On Sat, 2009-11-21 at 19:00 +0100, Francesco Pietra wrote:
>>>> Hi:
>>>
>>> francesco,
>>>
>>> [...]
>>>
>>>> If cgsolvate.tcl is added to
>>>>
>>>> /usr/local/lib/vmd/plugins/noarch/tcl/solvate1.3
>>>>
>>>> it is not seen by the command
>>>>
>>>> package require ...
>>>
>>> no surprise. this is not how these things work in tcl.
>>>
>>>>
>>>> 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.
>>>
>>> again, this is perfect tcl behavior. the script you want to
>>> use is a hack, and an ugly one to boot, as it contains hardcoded
>>> paths to directories on the schulten group NFS server, so it
>>> would have required some editing. the clean solution would
>>> have been to rename all references of solvate to cgsolvate.
>>> the solvate package has since evolved and augmented with additional
>>> features. from the cvs changelog, it looks as if it predates
>>> the optimizations for systems containing millions of atoms
>>> that were done in january and febuary of 2009 and also the
>>> support for arbitrary solvents that was added in january 2007.
>>> so the hack is quite old, actually.
>>>
>>> the fact that the current solvate package allows you
>>> to use an arbitrary solvents, should make this hacked
>>> version not really needed anymore.
>>>
>>>> My first question is: should I downgrade to VMD 1.8.6? Anton's files
>>>> are not that old, 31 AUG 2009.
>>>
>>> remember that those are copies and thus most likely
>>> you see the time they were copied over. it doesn't say
>>> anything about its real age which could well be four
>>> years or more (see above).
>>>
>>>> My second question: are the above files for lipids enough for my task?
>>>
>>> why don't you try and see?
>>>
>>>> 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?
>>>
>>> yeah, it just makes sense to me. it is much easier to merge components
>>> later, and you make it easier for the CG tool to get it right. it is
>>> also easier to identify and debug problems.
>>>
>>> axel.
>>>
>>>>
>>>> Thanks for answering
>>>>
>>>> francesco pietra
>>> --
>>> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
>>> Institute for Computational Molecular Science
>>> College of Science and Technology
>>> Temple University, Philadelphia PA, USA.
>>>
>>>
>>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>

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