<div>Hi Justin</div>
<div> </div>
<div>I had pasted below what i got after executing make command. any help is highly appreciated.</div>
<div> </div>
<div>cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-lo<br>ops -std=gnu99 -o grompp.exe grompp.o  -L/cygdrive/c/Packages/fftw/lib/CPPFlAGS=<br>-I/cygdrive/c/Packages/fftw/include/ ./.libs/libgmxpreprocess.a -L/lib -L/usr/li<br>
b ../mdlib/.libs/libmd.a /cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/lib<br>gmx.a ../gmxlib/.libs/libgmx.a /usr/lib/libxml2.dll.a -lz /usr/lib/libfftw3f.dll<br>.a /usr/lib/libSM.dll.a /usr/lib/libuuid.dll.a /usr/lib/libintl.dll.a /usr/lib/l<br>
ibiconv.dll.a /usr/lib/libICE.dll.a /usr/lib/libX11.dll.a /usr/lib/libxcb.dll.a<br>/usr/lib/libXau.dll.a /usr/lib/libXdmcp.dll.a<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.text+0xa6): undefined reference to `_nb_kernel_ia3<br>
2_3dnow_test_asm&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x40): undefined reference to `_nb_kernel010<br>_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>
w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x48): undefined reference to `_nb_kernel030<br>_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x4c): undefined reference to `_nb_kernel100<br>
_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x50): undefined reference to `_nb_kernel101<br>_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>
w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x54): undefined reference to `_nb_kernel102<br>_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x60): undefined reference to `_nb_kernel110<br>
_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x64): undefined reference to `_nb_kernel111<br>_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>
w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x68): undefined reference to `_nb_kernel112<br>_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.rdata+0xec): undefined reference to `_nb_kernel300<br>
_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.rdata+0xf0): undefined reference to `_nb_kernel301<br>_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>
w.o):nb_kernel_ia32_3dnow.c:(.rdata+0xf4): undefined reference to `_nb_kernel302<br>_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x100): undefined reference to `_nb_kernel31<br>
0_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x104): undefined reference to `_nb_kernel31<br>1_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>
w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x108): undefined reference to `_nb_kernel31<br>2_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x128): undefined reference to `_nb_kernel33<br>
0_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x12c): undefined reference to `_nb_kernel33<br>1_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_3dno<br>
w.o):nb_kernel_ia32_3dnow.c:(.rdata+0x130): undefined reference to `_nb_kernel33<br>2_ia32_3dnow&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.text+0xa6): undefined reference to `_nb_kernel_ia32_ss<br>
e_test_asm&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x40): undefined reference to `_nb_kernel010_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0x48): undefined reference to `_nb_kernel030_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x4c): undefined reference to `_nb_kernel100_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x50): undefined reference to `_nb_kernel101_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0x54): undefined reference to `_nb_kernel102_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x58): undefined reference to `_nb_kernel103_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x5c): undefined reference to `_nb_kernel104_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0x60): undefined reference to `_nb_kernel110_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x64): undefined reference to `_nb_kernel111_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x68): undefined reference to `_nb_kernel112_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0x6c): undefined reference to `_nb_kernel113_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x70): undefined reference to `_nb_kernel114_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x88): undefined reference to `_nb_kernel130_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0x8c): undefined reference to `_nb_kernel131_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x90): undefined reference to `_nb_kernel132_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x94): undefined reference to `_nb_kernel133_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0x98): undefined reference to `_nb_kernel134_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x9c): undefined reference to `_nb_kernel200_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xa0): undefined reference to `_nb_kernel201_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0xa4): undefined reference to `_nb_kernel202_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xa8): undefined reference to `_nb_kernel203_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xac): undefined reference to `_nb_kernel204_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0xb0): undefined reference to `_nb_kernel210_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xb4): undefined reference to `_nb_kernel211_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xb8): undefined reference to `_nb_kernel212_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0xbc): undefined reference to `_nb_kernel213_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xc0): undefined reference to `_nb_kernel214_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xd8): undefined reference to `_nb_kernel230_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0xdc): undefined reference to `_nb_kernel231_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xe0): undefined reference to `_nb_kernel232_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xe4): undefined reference to `_nb_kernel233_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0xe8): undefined reference to `_nb_kernel234_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xec): undefined reference to `_nb_kernel300_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xf0): undefined reference to `_nb_kernel301_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0xf4): undefined reference to `_nb_kernel302_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xf8): undefined reference to `_nb_kernel303_ia3<br>
2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0xfc): undefined reference to `_nb_kernel304_ia3<br>2_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0x100): undefined reference to `_nb_kernel310_ia<br>32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x104): undefined reference to `_nb_kernel311_ia<br>
32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x108): undefined reference to `_nb_kernel312_ia<br>32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0x10c): undefined reference to `_nb_kernel313_ia<br>32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x110): undefined reference to `_nb_kernel314_ia<br>
32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x128): undefined reference to `_nb_kernel330_ia<br>32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0x12c): undefined reference to `_nb_kernel331_ia<br>32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x130): undefined reference to `_nb_kernel332_ia<br>
32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x134): undefined reference to `_nb_kernel333_ia<br>32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0x138): undefined reference to `_nb_kernel334_ia<br>32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x13c): undefined reference to `_nb_kernel400_ia<br>
32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>o):nb_kernel_ia32_sse.c:(.rdata+0x140): undefined reference to `_nb_kernel410_ia<br>32_sse&#39;<br>/cygdrive/c/Packages/gromacs-4.0.5/src/gmxlib/.libs/libgmx.a(nb_kernel_ia32_sse.<br>
o):nb_kernel_ia32_sse.c:(.rdata+0x144): undefined reference to `_nb_kernel430_ia<br>32_sse&#39;<br>collect2: ld returned 1 exit status<br>make[3]: *** [grompp.exe] Error 1<br>make[3]: Leaving directory `/cygdrive/c/Packages/gromacs-4.0.5/src/kernel&#39;<br>
make[2]: *** [all-recursive] Error 1<br>make[2]: Leaving directory `/cygdrive/c/Packages/gromacs-4.0.5/src&#39;<br>make[1]: *** [all] Error 2<br>make[1]: Leaving directory `/cygdrive/c/Packages/gromacs-4.0.5/src&#39;<br>make: *** [all-recursive] Error 1</div>

<div> </div>
<div>Regards</div>
<div>Vinoth</div>
<div><br><br> </div>
<div class="gmail_quote">On Mon, Oct 11, 2010 at 4:03 PM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>vinothkumar mohanakrishnan wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Its not clear to me what you are asking. if iam right the above message is the configure command that i used during installation of gromacs.<br>
 <br></blockquote><br></div>The error message you posted from make is incomplete.  There should be lines immediately above the &quot;collect2: Id returned 1 exit status&quot; line that indicate the actual error message.  Please post that information.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Regards<br>Vinoth 
<div class="im"><br><br>On Mon, Oct 11, 2010 at 12:03 PM, Mark Abraham &lt;<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a> &lt;mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>&gt;&gt; wrote:<br>
<br><br><br>   ----- Original Message -----<br>   From: vinothkumar mohanakrishnan &lt;<a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a><br></div>
<div class="im">   &lt;mailto:<a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a>&gt;&gt;<br>   Date: Monday, October 11, 2010 17:12<br>   Subject: Re: [gmx-users] Reg: Installing gromacs in cygwin<br>
   To: Discussion list for GROMACS users &lt;<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
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<div class="h5">   &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;&gt;<br><br>    &gt; Hi mark<br>    &gt;       &gt; I have installed cygwin 1.7.7(the latest version) and i want to<br>
   install only gromacs 4.0.5 (for scientific continuity).any help is<br>   highly appreciated.<br><br>   OK, so like I asked last time, what&#39;s above the message you quoted?<br><br>   Mark<br><br>    &gt;       &gt; Regards<br>
    &gt; Vinoth<br>    &gt;<br>    &gt; On Mon, Oct 11, 2010 at 11:20 AM, Mark Abraham<br>   &lt;<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>&gt; wrote:<br><br>        &gt;<br>        &gt;<br>
        &gt; ----- Original Message -----<br>        &gt; From: vinothkumar mohanakrishnan &lt;<a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a>&gt;<br>        &gt; Date: Monday, October 11, 2010 16:29<br>
        &gt; Subject: [gmx-users] Reg: Installing gromacs in cygwin<br>        &gt; To: Discussion list for GROMACS users &lt;<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt;<br>        &gt;<br>
        &gt; &gt; Hi<br>        &gt; &gt;           &gt; &gt; I am installing gromacs-4.0.5<br>        &gt;<br>        &gt; That version&#39;s a few years old, and unless you need<br>       scientific continuity, you should install the latest version.<br>
        &gt;<br>        &gt;<br>        &gt; &gt; in windows using cygwin and i followed th procedure<br>       described in the link<br>       <a href="http://lists.gromacs.org/pipermail/gmx-users/2009-September/044792.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2009-September/044792.html</a>.<br>
       there is no problem with fftw-3.2.2 installation. while<br>       insatlling gromacs at first i gave the command (as said in the<br>       link above)<br>        &gt; &gt;           &gt; &gt; ./configure --prefix=/cygdrive/c/Packages/Gromacs<br>
       --enable-shared<br>        &gt; &gt;                  LDFLAGS=&#39;-L/cygdrive/c/Packages/fftw/lib/&#39;<br>        &gt; &gt;                         CPPFLAGS=&#39;-I/cygdrive/c/Packages/fftw/include/&#39;<br>        &gt; &gt;           &gt; &gt; and then i gave the command *make* and i am getting the<br>
       error message as one given below. any help is highly appreciated.<br>        &gt; &gt;           &gt; &gt; collect2: Id returned 1 exit status<br>        &gt; &gt; make[3]: *** [grompp.exe] Error 1<br>        &gt; &gt; make[3]: Leaving directory<br>
       &#39;/cygdrive/c/Packages/gromacs-4.0.5/src/kernel&#39;<br>        &gt; &gt; make[2]: *** [all-directory] Error 1<br>        &gt; &gt; make[2]: Leaving directory<br>       &#39;/cygdrive/c/Packages/gromacs-4.0.5/src&#39;<br>
        &gt; &gt; make[1]: *** [all] Error 2<br>        &gt; &gt; make[1]: Leaving directory<br>       &#39;/cygdrive/c/Packages/gromacs-4.0.5/src&#39;<br>        &gt; &gt; make: *** [all-recursive] Error 1<br>        &gt;<br>
        &gt; What&#39;s above that? Is this a recent cygwin installation?<br>        &gt;<br>        &gt; Mark<br>        &gt;<br>        &gt; --<br>        &gt; gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
        &gt; <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>        &gt; Please search the archive at<br>       <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
        &gt; Please don&#39;t post (un)subscribe requests to the list. Use the<br>        &gt; www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
        &gt; Can&#39;t post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br>    &gt;<br>    &gt; --<br>    &gt; gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
</div></div>   &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt; 
<div class="im"><br>    &gt; <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>    &gt; Please search the archive at<br>    &gt; <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
    &gt; Please don&#39;t post (un)subscribe requests to the list. Use the<br>    &gt; www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
   &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;. 
<div class="im"><br>    &gt; Can&#39;t post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br>   --<br>   gmx-users mailing list    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
</div>   &lt;mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>&gt; 
<div class="im"><br>   <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" 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" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
   Please don&#39;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" target="_blank">gmx-users-request@gromacs.org</a><br></div>   &lt;mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>&gt;. 
<div class="im"><br>   Can&#39;t post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br></div></blockquote><br>-- <br>========================================<br>
<br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><font color="#888888">-- <br>
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Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don&#39;t post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can&#39;t post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></div></div></blockquote></div><br>