[gmx-users] Problem with setting vsite=aromatics on OPLSAA

Berk Hess gmx3 at hotmail.com
Thu Nov 6 15:22:39 CET 2008


I fixed the bug in pdb2gmx. This bug would cause a segv with vsite aromatics in larger proteins.
I also fixed the issue in mdrun with vsite aromatics.

So now vsite aromatics will be fully functional in 4.0.1.


From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Problem with setting vsite=aromatics on OPLSAA
Date: Tue, 4 Nov 2008 15:18:06 +0100


There is indeed a bug in pdb2gmx.
I did not write this code, so I don't know exactly what is wrong.

But today somebody also mailed about a problem in the 4.0 mdrun 
with vsite aromatics.

My opinion is that it is not worth to try to keep supporting this feature,
because the time step is not much larger than the 4 or 5 fs you
can reach with only -vsite h and the heavy hydrogens will also slightly
slow down your dynamics.


> From: genesup at gmail.com
> To: gmx-users at gromacs.org
> Date: Tue, 4 Nov 2008 16:36:19 +0300
> Subject: [gmx-users] Problem with setting vsite=aromatics on OPLSAA
> Hello,
> when I run the following command:
> pdb2gmx -f 1klc.192722.pdb -o 1klc.192722 -p 1klc.192722 -vsite
> aromatics
> the progran starts generating topology but in the end I get
> "Segmentation fault". No notes, no warnings though.
> Is it possible to use dummy aromatics with OPLSAA?
> Thanks
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