VMD-L Mailing List

From: Behnam Ghalami (ghalamichoobar_at_gmail.com)
Date: Fri Nov 09 2018 - 13:27:27 CST

Dear Peter
Thank you for the answer.It was great help!!!
Sincerely,
Behnam Ghalami Choobar

On Fri, Nov 9, 2018 at 3:45 PM Peter Kroon <p.c.kroon_at_rug.nl> wrote:

> Hi all,
>
>
> the martini script *should* work. It hasn't seen actual maintenance (the
> guy who made it finished his PhD 4 years ago, and since left the lab),
> so you may need to change a few things, such as the path to the `gmx
> dump` executable.
>
> I personally never use it to parse .top files (but others in the lab
> do), but I have good experience with having it parse the tpr files.
>
>
> Peter
>
> On 08-11-18 18:45, Vermaas, Joshua wrote:
> > Do the martini scripts work? Those are newer, and while they are
> > originally designed for martini, they may also work for your use case.
> > VMD recompilation is usually a poor use of a scientists time, I only
> > mention it for the folks that do enjoy a challenge, or have prior
> > compiling experience. The best guide I've seen for compiling VMD
> > is
> https://robinbetz.com/blog/2015/01/08/compiling-vmd-with-python-support/
> >
> > -Josh
> >
> >
> >
> > On 2018-11-08 08:00:35-07:00 Behnam Ghalami wrote:
> >
> > Dear Josh
> > Many thanks for your kind reply. I'm trying to simulate
> > electrolytes employing OPLS-AA. I tested top2psf script but It
> > didn't work. I'm going to carry out your suggestion about
> > compiling my own VMD but I don't have any experience about it. I
> > would appreciate if you could introduce me references regarding
> > compiling VMD.
> > Thanks in advance.
> > Sincerely yours,
> > Behnam Ghalami Choobar
> >
> > On Wed, Nov 7, 2018 at 9:39 PM Vermaas, Joshua
> > <Joshua.Vermaas_at_nrel.gov <mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
> >
> > Hi Behnam,
> >
> > .gro files don't contain bond information, so VMD guesses
> > based on atomic distances. I'm going to guess this is a coarse
> > grained system, since the atomic distances are much greater in
> > those systems and VMD in that case tends not to work very
> > well. Basically, you need to use your .top file or .tpr file
> > to produce a file that VMD can read in for the bond
> > information. Some options include:
> >
> > Using top2psf to make a psf
> > file.
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/top2psf.pl
> > <
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2Fscript_library%2Fscripts%2Ftop2psf%2Ftop2psf.pl&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C7f211212f586453616d008d6458aee02%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636772860346070985&sdata=WViYrt0sQLFlcgXur%2F1l5fpk36ktWXbEw%2B1btwnc1ZA%3D&reserved=0
> >
> >
> > If you are using a coarse grained system, the Martini folks
> > have some tools to make visualization easier:
> >
> http://cgmartini.nl/index.php/tutorials-general-introduction/cgviz
> > <
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcgmartini.nl%2Findex.php%2Ftutorials-general-introduction%2Fcgviz&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C7f211212f586453616d008d6458aee02%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636772860346070985&sdata=ZDNV934b7xodtPmratUDMu96Faw2jOV9flOGmuBHSew%3D&reserved=0
> >
> > http://www.cgmartini.nl/index.php/rb
> > <
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cgmartini.nl%2Findex.php%2Frb&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C7f211212f586453616d008d6458aee02%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636772860346070985&sdata=li5Z6sgwYFzXf8TkyIQcekGdsomUb0hvQOE6VTfBreE%3D&reserved=0
> >
> >
> > If you are crazy like me and compile your own VMD, you can use
> > either my .tpr loader
> > (https://github.com/jvermaas/vmd-tprreader)
> > <
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjvermaas%2Fvmd-tprreader)&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C7f211212f586453616d008d6458aee02%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636772860346070985&sdata=NJp8EWjTW6fkKoeEBOAZIh3fWREn%2FA0i897ASG6Sfck%3D&reserved=0
> >
> > or the .tng support VMD includes to load gromacs files directly--0000000000001fa4b9057a4058c3--