VMD-L Mailing List

From: Peter Kroon (p.c.kroon_at_rug.nl)
Date: Fri Nov 09 2018 - 06:15:55 CST

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.
>
> -Josh Vermaas
>  
>
> On 2018-11-07 02:30:56-07:00 owner-vmd-l_at_ks.uiuc.edu
> <mailto:owner-vmd-l_at_ks.uiuc.edu> wrote:
>
> Dear all
> Unfortunately when I import gromacs output .gro into VMD,
> it does not recognize residues properly and displays
> molecules as broken ones. How can I solve this problem?
> Thanks in advance.
> Looking forward to hearing from you.
> Sincerely,
> Behnam Ghalami Choobar
>
> --
> Behnam Ghalami Choobar
> PhD Candidate in Chemical Engineering
> Amirkabir University of Technology, Tehran-Iran
>
>
>
> --
> Behnam Ghalami Choobar
> PhD Candidate in Chemical Engineering
> Amirkabir University of Technology, Tehran-Iran
>