Berk, 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! Dongsheng On Fri, 2006-07-14 at 10:23 +0200, Berk Hess wrote: > > > >From: Dongsheng Zhang <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> > >To: Discussion list for GROMACS users <gmx-users@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. > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
