[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units

Berk Hess gmx3 at hotmail.com
Tue Jul 17 10:03:11 CEST 2007

>From: "Frankie Montenegro" <frankie.montenegro at gmail.com>
>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] a) rlist vs rvdw/rcoulomb size confusion,and b) 
>reduced units
>Date: Tue, 17 Jul 2007 03:41:46 -0400
>>So if you box size is 5 (as you say) and your cut-off is 1, then you
>>should not get an error.
>>So one of the two things is wrong.
>>Maybe you made a pdb file with box 5?
>>pdb is in Angstrom, while Gromacs uses nm, so there is a conversion
>>factor of 0.1.
>That's what it was. Thanks a bunch. A follow-up question:
>Gromacs Manual, page 142 in Chapter 7, Run parameters and Programs:
>                vdwtype: User
>                               When you want to use LJ correction, make 
>                               that rvdw corresponds to the cut-off in
>the user-defined
>                               function.
>End of quote.
>But my potential has three different vdw cutoffs for three different
>Is there a way to account for all of them?
>If not,  I want to set it to the greatest one, correct? I can't see
>that option having any unwanted consequences, assuming first column of
>table.xvg, table_ii_ii.xvg and table_jj_jj.xvg stays within rvdw+1.
>Thanks again,

I think that what you want is inconsistent.
If you want dispersion correction this means that in principle you do not 
cut-off's. You only use cut-off's for computational reasons.
If this is the case you can just make your three cut-off's identical.
You can just fill your table with values beyond your current cut-off,
which you have to do anyhow, since there are no "exact distance" cut-offs in 
unless you use nstlist=1.


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