<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span><var id="yui-ie-cursor"></var>Dear All,</span></div><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div id="yiv1715806418"><div><div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><div><span></span> </div><div><span>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?</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Acoot.</span></div><div><span></span> </div><div><span></span> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x6c5c): more undefined references to `_bool_names' follow</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x7f40): undefined reference to `_read_first_frame'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x7f6c): undefined reference to `_read_first_frame'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x7fce): undefined reference to
`_read_next_frame'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x7fe7): undefined reference to `_read_next_frame'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8014): undefined reference to `_close_trj'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8037): undefined reference to `_close_trj'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x816f): undefined reference to `_open_enx'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x818d): undefined reference to `_open_enx'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x81ab): undefined reference to `_do_enxnms'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x81d0): undefined reference to `_do_enxnms'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8235): undefined reference to `_save_calloc'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8268): undefined reference to
`_save_calloc'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x829e): undefined reference to `_save_calloc'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x839b): undefined reference to `_gmx_strncasecmp'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8b79): undefined reference to `_save_calloc'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8ba7): undefined reference to `_save_calloc'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8bbf): undefined reference to `_do_enx'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8bd8): undefined reference to `_do_enx'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8c79): undefined reference to `_close_enx'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8c88): undefined reference to `_close_enx'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8c94): undefined reference to
`_free_enxframe'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8cb8): undefined reference to `_save_free'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8cc0): undefined reference to `_free_enxframe'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8ce0): undefined reference to `_save_free'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x8e9f): undefined reference to `_gmx_step_str'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x90ef): undefined reference to `__gmx_error'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x91ed): undefined reference to `_save_calloc'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x94f7): undefined reference to `_save_free'</div><div> </div><div>.libs/tpbcmp.o:tpbcmp.c:(.text+0x98a5): undefined reference to `_debug'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0xd): undefined reference to
`_debug'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x6e): undefined reference to `_debug'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0xe1): undefined reference to `_debug'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x14e): undefined reference to `_debug'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x1c2): more undefined references to `_debug' follow</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x253): undefined reference to `_gmx_strncasecmp'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x2b0): undefined reference to `_gmx_strncasecmp'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x1264): undefined reference to `_debug'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x1304): undefined reference to
`_gmx_strncasecmp'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x136c): undefined reference to `_gmx_strncasecmp'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x33db): undefined reference to `_debug'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x3430): undefined reference to `_save_calloc'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x345f): undefined reference to `_save_calloc'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x3471): undefined reference to `_interaction_function'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x347c): undefined reference to `_interaction_function'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x3b01): undefined reference to `_save_free'</div><div> </div><div>.libs/vsite_parm.o:vsite_parm.c:(.text+0x3b13): undefined reference to `_interaction_function'<var
id="yiv1715806418yui-ie-cursor"></var><br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="yiv1715806418hr"></div> <b><span style="font-weight: bold;">From:</span></b> Tsjerk Wassenaar <tsjerkw@gmail.com><br> <b><span style="font-weight: bold;">To:</span></b> Acoot Brett <acootbrett@yahoo.com> <br><b><span style="font-weight: bold;">Cc:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Monday, 19 March 2012 7:27 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] on "tcoupl= V-rescale"<br> </font> </div> <br>Hi
Acoot,<br><br>Please keep discussions on the list.<br>This issue came across just last week. You should be able to install<br>gromacs 4.5.5 under cygwin:<br><br><a href="http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO" rel="nofollow" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO</a><br><br>Check the recent list archives for more hints on how to get it done.<br><br>Cheers,<br><br>Tsjerk<br><br><br>On Mon, Mar 19, 2012 at 10:21 AM, Acoot Brett <<a href="mailto:acootbrett@yahoo.com" rel="nofollow" target="_blank" ymailto="mailto:acootbrett@yahoo.com">acootbrett@yahoo.com</a>> wrote:<br>> Dear Tsjerk,<br>><br>> I have tried to install the latest version in my cygwin, but it cannot be<br>> installed. Only the previous versions of gromacs can be installed in my<br>> cygwin. Thus I hope I can get an explaination from you.<br>><br>> Cheers,<br>><br>>
Acoot<br>><br>> From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" rel="nofollow" target="_blank" ymailto="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>> To: Acoot Brett <<a href="mailto:acootbrett@yahoo.com" rel="nofollow" target="_blank" ymailto="mailto:acootbrett@yahoo.com">acootbrett@yahoo.com</a>>; Discussion list for GROMACS users<br>> <<a href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Sent: Monday, 19 March 2012 7:17 PM<br>> Subject: Re: [gmx-users] on "tcoupl= V-rescale"<br>><br>> Hey Acoot,<br>> Hy not try the latest version, or at least the version the tutorial was made<br>> for?<br>> Cheers,<br>> Tsjerk<br>><br>> On Mar 19, 2012 10:13 AM, "Acoot Brett" <<a href="mailto:acootbrett@yahoo.com" rel="nofollow" target="_blank"
ymailto="mailto:acootbrett@yahoo.com">acootbrett@yahoo.com</a>> wrote:<br>><br>> Dear All,<br>><br>> I am using the GROMACS 3.3.3 to practice the lysozyme tutorial of Justin<br>> Lemkul<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html" rel="nofollow" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html</a>.<br>><br>> For each .mdp used in the tutorial, there is "tcoupl = V-rescale".<br>><br>> However if we do not change the value of tcoupl in any .mdp related step, it<br>> always fails, and it suggest "ERROR: invalid enum 'V-rescale' for variable<br>> tcoupl, using 'No'. Next time use one of: 'No' 'Berendsen' 'Nose-Hoover'<br>> 'yes' 'Andersen' 'Andersen-interval'".<br>><br>> When I change the tcoupl=no, it always works.<br>><br>> Will you please tell me in which situation use 'No'
'Berendsen'<br>> 'Nose-Hoover' 'yes' 'Andersen' 'Andersen-interval'" separately.<br>><br>> I am looking forward to getting your reply.<br>><br>> Cheers,<br>><br>> Acoot<br>><br>><br>> --<br>> gmx-users
mailing list <a href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" rel="nofollow" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" rel="nofollow" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" rel="nofollow"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>><br>><br>><br><br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br><br>post-doctoral researcher<br>Molecular
Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br><br><br> </div> </div> </div></div></div><meta content="on" http-equiv="x-dns-prefetch-control"><br><br> </div> </div> </div></body></html>