[gmx-users] pull code : cvs vs gmx3.1.5_pre1
taeho.kim at utoronto.ca
Tue Jun 24 21:01:01 CEST 2003
My previous mail seems unreadable, so I post it again.
I was wondering whether the pull code (Gromac3.1.5_pre1 ver) can be run on a dual CPU Mac. or 3.1.5_pre1 works fine only on a single process machine.
Do I have to install a current cvs ver to run a job on dual CPU ?
I attempted to install and run the CVS version as of June 18th, everything compiled nicely. However, when I tried to run gmxdemo i received an error during the genbox processing:
*** malloc_zone_calloc: arguments too large: -2,4
Fatal error: calloc for grid->index (nelem=-2, elsize=4, file nsgrid.c, line 77): No such file or directory
Also it says "box margin = 0" which is unusual
(running version fftw-2.1.3 on Mac OS X)
On Linux system without enable-mpi, I had similar problem too .
보낸 사람: Kay Gottschalk <kay.gottschalk at weizmann.ac.il>
받는 사람: gmx-users at gromacs.org <gmx-users at gromacs.org>
날짜: 2003년 6월 24일 화요일 오전 8:52
제목: Re: [gmx-users] g_sas
>Can I just install g_sas from the current CVS code or do I have to
>install everything new? If the former, what do I have to do? Thanks a
>lot for your help,
>On Tuesday, June 24, 2003, at 02:57 AM, Berk Hess wrote:
>>> Hi there, when i am running
>>> g_sas -f full -s full -i -minarea 0.15 -oa
>>> I get as surface area 0.23 for atom 5 in atomarea.xvg, but atom 5
>>> does not appear in surfat.itp - similar things are true for very many
>>> atoms. That means that atoms, which should be surface atoms, are not
>>> accounted for in the surfat.itp, which as far as I know should entail
>>> all surface atoms. Do I do anything wrong here ?
>>> Thanks for your help,
>> The -r and -oa (resarea and atomarea) output of g_sas has always been
>> The normal -o output is correct though.
>> The only way to get correct atom areas is to use the current CVS code.
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