[gmx-users] Some problems with tools

David van der Spoel spoel at xray.bmc.uu.se
Sat Jul 7 19:24:53 CEST 2007

Дмитрий Егоров wrote:
> 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?
this has probably been fixed in CVS as well.

> 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?
I don't understand what the problem is.

> 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?
genion ?

> Thank you very much for your attention to my problem.
> Dmitry Yegorov.
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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