[gmx-users] program crashes when -table option used

Dongsheng Zhang dong at pampas.chem.purdue.edu
Fri Jul 14 16:23:59 CEST 2006


Thank you very much for your suggestion. After I extend the table
extension to 2.0nm, the program works fine now.

Initially the cut_off is 1.4 nm, the table extension is 1.0nm, so my
table is for the interactions whose distance is within 2.5nm. I thought
it is long enough. Could you please explain to me why gromacs compares
the distance between 1 and 4 to the table extension parameter, not the
whole table length (cut-off + table extension)? 

I need to use multiple tables for pair interaction (1-4 interaction)
calculations. Currently gromacs can only read one table for pair
interactions. I am thinking to take advantage of the COUL term in
table.xvg because there is no COUL interaction in my coarse-grained
model. The only thing I need to modify in the source code is to switch
the calculation of pair interaction to the calculation of COUL term. If
you think this is a good approach, could you please tell me how to
modify it?

All the best!


On Fri, 2006-07-14 at 10:23 +0200, Berk Hess wrote:
> >From: Dongsheng Zhang <dong at pampas.chem.purdue.edu>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] program crashes when -table option used
> >Date: Fri, 14 Jul 2006 02:13:54 -0400
> >
> >Yang Ye,
> >
> >I just can't understand why the program ran fine in one way, but crashed
> >in another way. If the two coordinates file are the same, how come did
> >the second run give me large value of LJ_14? If it is possible, I can
> >give you my two tpr file, you can do the test.
> >
> The large LJ_14 value could mean that a 1-4 interaction
> pair went beyond the table length.
> Did you get warnings about this?
> What is your cut-off and table-extension?
> >I used a coarse grained model, dt = 0.002. I don't think it is too large
> >for a monomer.
> >
> >By the way, it seems David has not told us how to input multiple
> >tablep.xvg files, right?
> You can not have multiple tablep.xvg files.
> You can only use one, which is applied to all 1-4 interactions.
> Berk.
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