VMD-L Mailing List
From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Nov 08 2018 - 11:45:59 CST
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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 If you are using a coarse grained system, the Martini folks have some tools to make visualization easier:
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
http://cgmartini.nl/index.php/tutorials-general-introduction/cgviz
http://www.cgmartini.nl/index.php/rb
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
