[gmx-users] Some problems with tools

[Дмитрий Егоров]

Dear Gromacs list members,
I just have problem with using some tools included in the Gromacs.

First, g_rdf probably incorrectly compiled under gcc-4.1.x. At least I got freezed on zero frame reading binary of the program in 3 cases : in SuSe-10.1 by my own compilation, Debian 4.0 "Etch" - in my own compilation and also in precompiled package delivered within this Debian release. GCC-3.4 gives normally reading binary, but options -b -e probably work incorrectly - for 50 ps simulation frames upper 40.1 ps are unaccecible. Why?

When I use genbox separately for two -vdwd of 0.18691 and 0.19689 in same tip3p box I get may be strange difference in cut-offs - 0.33 in first case and 0.59067  - in second. Is it all right?

And just another theme. I want obtain box of one ion in the center of previously equilibrated tip3p box with minimal possible number of deleted water molecules for subsequent NVT simulation for obtaining most reliable first pics in rdf ion-OW and ion-HW. What a receipt?

Thank you very much for your attention to my problem.

Dmitry Yegorov.