[gmx-developers] Re: Bug in x2top, gromacs-4.0.5

Vitaly V. Chaban vvchaban at gmail.com
Mon Jul 13 10:16:37 CEST 2009

Hi Wolfram,

The bug in x2top is actually present with nanotubes starting from version
3.3.3. It really works fine well in 3.3.1 (3.3.2 was never used by me).

Please report the bug to the bugzilla. Sorry, I didn't find a time to fo
this for a year. :(

~ Vitaly

> Hello Everybody,
> I guess I found a bug in x2top. I was trying to generate a topology
> for a carbon nanotube, what works fine with the x2top coming with
> gromacs-3.3.x. If I try to run with the gromacs-4.0.5 x2top instead
> the program will hang for days, running at 100% cpu but showing no
> progress at all.
> Looking at the source code, there are quite a lot of changes between
> the two versions, so I can't really tell what's causing the problem.
> The pdb file used to generate the topology can be found under
> http://www.picb.ac.cn/graeter/files_wolfram/tube.pdb
> There are also little extras for x2top to run correctly on the nanotube:
> http://www.picb.ac.cn/graeter/files_wolfram/ffgmxbon.itp
> http://www.picb.ac.cn/graeter/files_wolfram/ffencadv.n2t
> The procedure is also described on http://cs86.com/index.html
> And the command was:
> x2top -f tube.pdb -o tube.top -r tube.rtp -ff select
> using
> 8: Encad all-atom force field, using scaled-down vacuum charges
> (the bug also happens when trying to use OPLS)
> Best regards,
> Wolfram
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, mob.: +38-097-8259698
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