[gmx-users] on installation of gromacs 455

Mon Mar 19 10:49:16 CET 2012

Dear All,

When I install 455 under cygwin, I got a series of following error message in the gromacs make step. Will you please give me some suggestions on how to avoid it?

Cheers,

Acoot.

.libs/tpbcmp.o:tpbcmp.c:(.text+0x6c5c): more undefined references to `_bool_names' follow

.libs/tpbcmp.o:tpbcmp.c:(.text+0x7f40): undefined reference to `_read_first_frame'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x7f6c): undefined reference to `_read_first_frame'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x7fce): undefined reference to `_read_next_frame'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x7fe7): undefined reference to `_read_next_frame'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8014): undefined reference to `_close_trj'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8037): undefined reference to `_close_trj'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x816f): undefined reference to `_open_enx'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x818d): undefined reference to `_open_enx'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x81ab): undefined reference to `_do_enxnms'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x81d0): undefined reference to `_do_enxnms'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8235): undefined reference to `_save_calloc'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8268): undefined reference to `_save_calloc'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x829e): undefined reference to `_save_calloc'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x839b): undefined reference to `_gmx_strncasecmp'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8b79): undefined reference to `_save_calloc'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8ba7): undefined reference to `_save_calloc'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8bbf): undefined reference to `_do_enx'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8bd8): undefined reference to `_do_enx'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8c79): undefined reference to `_close_enx'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8c88): undefined reference to `_close_enx'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8c94): undefined reference to `_free_enxframe'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8cb8): undefined reference to `_save_free'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8cc0): undefined reference to `_free_enxframe'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8ce0): undefined reference to `_save_free'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x8e9f): undefined reference to `_gmx_step_str'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x90ef): undefined reference to `__gmx_error'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x91ed): undefined reference to `_save_calloc'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x94f7): undefined reference to `_save_free'

.libs/tpbcmp.o:tpbcmp.c:(.text+0x98a5): undefined reference to `_debug'

.libs/vsite_parm.o:vsite_parm.c:(.text+0xd): undefined reference to `_debug'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x6e): undefined reference to `_debug'

.libs/vsite_parm.o:vsite_parm.c:(.text+0xe1): undefined reference to `_debug'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x14e): undefined reference to `_debug'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x1c2): more undefined references to `_debug' follow

.libs/vsite_parm.o:vsite_parm.c:(.text+0x253): undefined reference to `_gmx_strncasecmp'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x2b0): undefined reference to `_gmx_strncasecmp'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x1264): undefined reference to `_debug'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x1304): undefined reference to `_gmx_strncasecmp'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x136c): undefined reference to `_gmx_strncasecmp'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x33db): undefined reference to `_debug'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x3430): undefined reference to `_save_calloc'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x345f): undefined reference to `_save_calloc'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x3471): undefined reference to `_interaction_function'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x347c): undefined reference to `_interaction_function'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x3b01): undefined reference to `_save_free'

.libs/vsite_parm.o:vsite_parm.c:(.text+0x3b13): undefined reference to `_interaction_function'

________________________________
 From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: Acoot Brett <acootbrett at yahoo.com> 
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, 19 March 2012 7:27 PM
Subject: Re: [gmx-users] on "tcoupl= V-rescale"

Hi
 Acoot,

Please keep discussions on the list.
This issue came across just last week. You should be able to install
gromacs 4.5.5 under cygwin:

http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO

Check the recent list archives for more hints on how to get it done.

Cheers,

Tsjerk

On Mon, Mar 19, 2012 at 10:21 AM, Acoot Brett <acootbrett at yahoo.com> wrote:
> Dear Tsjerk,
>
> I have tried to install the latest version in my cygwin, but it cannot be
> installed. Only the previous versions of gromacs can be installed in my
> cygwin. Thus I hope I can get an explaination from you.
>
> Cheers,
>
> Acoot
>
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Sent: Monday, 19 March 2012 7:17 PM
> Subject: Re: [gmx-users] on "tcoupl= V-rescale"
>
> Hey Acoot,
> Hy not try the latest version, or at least the version the tutorial was made
> for?
> Cheers,
> Tsjerk
>
> On Mar 19, 2012 10:13 AM, "Acoot Brett" <acootbrett at yahoo.com> wrote:
>
> Dear All,
>
> I am using the GROMACS 3.3.3 to practice the lysozyme tutorial of Justin
> Lemkul
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html.
>
> For each .mdp used in the tutorial, there is "tcoupl = V-rescale".
>
> However if we do not change the value of tcoupl in any .mdp related step, it
> always fails, and it suggest "ERROR: invalid enum 'V-rescale' for variable
> tcoupl, using 'No'. Next time use one of: 'No' 'Berendsen' 'Nose-Hoover'
> 'yes' 'Andersen' 'Andersen-interval'".
>
> When I change the tcoupl=no, it always works.
>
> Will you please tell me in which situation use 'No' 'Berendsen'
> 'Nose-Hoover' 'yes' 'Andersen' 'Andersen-interval'" separately.
>
> I am looking forward to getting your reply.
>
> Cheers,
>
> Acoot
>
>
> --
> gmx-users
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular
 Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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