<br><br>
<div class="gmail_quote">On Tue, Apr 10, 2012 at 11:28 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="im">On 2012-04-10 12:02, Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Thank you for the reply. I do not have such files in my directory or in<br>my force field.<br></blockquote></div>
did you mean dos2unix?<br><br>try:<br>wc grompp.mdp<br>to count the number of lines. There should be may.<br>In fact grompp probably tells you which input file is erroneous, doesn't it?<br></blockquote>
<div> </div>
<div>It does not provide the information which file is this. I checked every file with wc -L and it does not exceed 100.</div>
<div>However I read that creating gurgle.dat - empty file may solve it. When I did it and process grmpp:</div>
<div> </div>
<div>Ignoring obsolete mdp entry 'title'<br>Generated 67161 of the 67161 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 1<br>Generated 49536 of the 67161 1-4 parameter combinations</div>
<div>WARNING: File is empty</div>
<div>*** glibc detected *** grompp: double free or corruption (!prev): 0x0000000001cf0480 ***<br>======= Backtrace: =========<br>/lib64/libc.so.6[0x30fc675296]<br>/lib64/libc.so.6(fclose+0x14d)[0x30fc665a1d]<br>grompp[0x5a5952]<br>
grompp[0x59ba29]<br>grompp[0x5a67bd]<br>grompp[0x5a661f]<br>grompp[0x5cb798]<br>grompp[0x5a7184]<br>grompp[0x41fd8c]<br>grompp[0x41fa38]<br>grompp[0x408a8d]<br>grompp[0x405422]<br>/lib64/libc.so.6(__libc_start_main+0xfd)[0x30fc61ecdd]<br>
grompp[0x404eaa]<br>======= Memory map: ========<br>00400000-00756000 r-xp 00000000 00:1f 107224920 /apps/gromacs/4.5.4/bin/grompp<br>00855000-00865000 rwxp 00355000 00:1f 107224920 /apps/gromacs/4.5.4/bin/grompp<br>
00865000-00894000 rwxp 00000000 00:00 0<br>01cde000-020a3000 rwxp 00000000 00:00 0 [heap]<br>30fbe00000-30fbe20000 r-xp 00000000 08:01 558856 /lib64/<a href="http://ld-2.12.so">ld-2.12.so</a><br>
30fc01f000-30fc020000 r-xp 0001f000 08:01 558856 /lib64/<a href="http://ld-2.12.so">ld-2.12.so</a><br>30fc020000-30fc021000 rwxp 00020000 08:01 558856 /lib64/<a href="http://ld-2.12.so">ld-2.12.so</a><br>
30fc021000-30fc022000 rwxp 00000000 00:00 0<br>30fc200000-30fc202000 r-xp 00000000 08:01 554053 /lib64/<a href="http://libdl-2.12.so">libdl-2.12.so</a><br>30fc202000-30fc402000 ---p 00002000 08:01 554053 /lib64/<a href="http://libdl-2.12.so">libdl-2.12.so</a><br>
30fc402000-30fc403000 r-xp 00002000 08:01 554053 /lib64/<a href="http://libdl-2.12.so">libdl-2.12.so</a><br>30fc403000-30fc404000 rwxp 00003000 08:01 554053 /lib64/<a href="http://libdl-2.12.so">libdl-2.12.so</a><br>
30fc600000-30fc786000 r-xp 00000000 08:01 558857 /lib64/<a href="http://libc-2.12.so">libc-2.12.so</a><br>30fc786000-30fc986000 ---p 00186000 08:01 558857 /lib64/<a href="http://libc-2.12.so">libc-2.12.so</a><br>
30fc986000-30fc98a000 r-xp 00186000 08:01 558857 /lib64/<a href="http://libc-2.12.so">libc-2.12.so</a><br>30fc98a000-30fc98b000 rwxp 0018a000 08:01 558857 /lib64/<a href="http://libc-2.12.so">libc-2.12.so</a><br>
30fc98b000-30fc990000 rwxp 00000000 00:00 0<br>30fca00000-30fca17000 r-xp 00000000 08:01 558858 /lib64/<a href="http://libpthread-2.12.so">libpthread-2.12.so</a><br>30fca17000-30fcc16000 ---p 00017000 08:01 558858 /lib64/<a href="http://libpthread-2.12.so">libpthread-2.12.so</a><br>
30fcc16000-30fcc17000 r-xp 00016000 08:01 558858 /lib64/<a href="http://libpthread-2.12.so">libpthread-2.12.so</a><br>30fcc17000-30fcc18000 rwxp 00017000 08:01 558858 /lib64/<a href="http://libpthread-2.12.so">libpthread-2.12.so</a><br>
30fcc18000-30fcc1c000 rwxp 00000000 00:00 0<br>30fce00000-30fce83000 r-xp 00000000 08:01 558867 /lib64/<a href="http://libm-2.12.so">libm-2.12.so</a><br>30fce83000-30fd082000 ---p 00083000 08:01 558867 /lib64/<a href="http://libm-2.12.so">libm-2.12.so</a><br>
30fd082000-30fd083000 r-xp 00082000 08:01 558867 /lib64/<a href="http://libm-2.12.so">libm-2.12.so</a><br>30fd083000-30fd084000 rwxp 00083000 08:01 558867 /lib64/<a href="http://libm-2.12.so">libm-2.12.so</a><br>
30fd200000-30fd215000 r-xp 00000000 08:01 558866 /lib64/libz.so.1.2.3<br>30fd215000-30fd414000 ---p 00015000 08:01 558866 /lib64/libz.so.1.2.3<br>30fd414000-30fd415000 r-xp 00014000 08:01 558866 /lib64/libz.so.1.2.3<br>
30fd415000-30fd416000 rwxp 00015000 08:01 558866 /lib64/libz.so.1.2.3<br>30fd600000-30fd607000 r-xp 00000000 08:01 558859 /lib64/<a href="http://librt-2.12.so">librt-2.12.so</a><br>
30fd607000-30fd806000 ---p 00007000 08:01 558859 /lib64/<a href="http://librt-2.12.so">librt-2.12.so</a><br>30fd806000-30fd807000 r-xp 00006000 08:01 558859 /lib64/<a href="http://librt-2.12.so">librt-2.12.so</a><br>
30fd807000-30fd808000 rwxp 00007000 08:01 558859 /lib64/<a href="http://librt-2.12.so">librt-2.12.so</a><br>30fe600000-30fe616000 r-xp 00000000 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1<br>
30fe616000-30fe815000 ---p 00016000 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1<br>30fe815000-30fe816000 rwxp 00015000 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1<br>
3106200000-3106347000 r-xp 00000000 08:01 738508 /usr/lib64/libxml2.so.2.7.6<br>3106347000-3106546000 ---p 00147000 08:01 738508 /usr/lib64/libxml2.so.2.7.6<br>3106546000-3106550000 rwxp 00146000 08:01 738508 /usr/lib64/libxml2.so.2.7.6<br>
3106550000-3106551000 rwxp 00000000 00:00 0<br>310d600000-310d616000 r-xp 00000000 08:01 558894 /lib64/<a href="http://libnsl-2.12.so">libnsl-2.12.so</a><br>310d616000-310d815000 ---p 00016000 08:01 558894 /lib64/<a href="http://libnsl-2.12.so">libnsl-2.12.so</a><br>
310d815000-310d816000 r-xp 00015000 08:01 558894 /lib64/<a href="http://libnsl-2.12.so">libnsl-2.12.so</a><br>310d816000-310d817000 rwxp 00016000 08:01 558894 /lib64/<a href="http://libnsl-2.12.so">libnsl-2.12.so</a><br>
310d817000-310d819000 rwxp 00000000 00:00 0<br>2b3cd1d8b000-2b3cd1d9e000 rwxp 00000000 00:00 0<br>2b3cd1dad000-2b3cd1dae000 rwxp 00000000 00:00 0<br>2b3cd1dae000-2b3cd2020000 r-xp 00000000 00:1f 91899538 /apps/intel/fc/9.1.045/lib/libimf.so<br>
2b3cd2020000-2b3cd211f000 ---p 00272000 00:1f 91899538 /apps/intel/fc/9.1.045/lib/libimf.so<br>2b3cd211f000-2b3cd2124000 rwxp 00271000 00:1f 91899538 /apps/intel/fc/9.1.045/lib/libimf.so<br>
2b3cd2124000-2b3cd2125000 rwxp 00000000 00:00 0<br>2b3cd2125000-2b3cd230a000 r-xp 00000000 00:1f 92286570 /apps/intel/ict/mpi/3.1.038/lib64/libmpi.so.3.2<br>2b3cd230a000-2b3cd240a000 ---p 001e5000 00:1f 92286570 /apps/intel/ict/mpi/3.1.038/lib64/libmpi.so.3.2<br>
2b3cd240a000-2b3cd241e000 rwxp 001e5000 00:1f 92286570 /apps/intel/ict/mpi/3.1.038/lib64/libmpi.so.3.2<br>2b3cd241e000-2b3cd245d000 rwxp 00000000 00:00 0<br>2b3cd245d000-2b3cd248d000 r-xp 00000000 00:1f 92286590 /apps/intel/ict/mpi/3.1.038/lib64/libmpigf.so.3.2<br>
2b3cd248d000-2b3cd258c000 ---p 00030000 00:1f 92286590 /apps/intel/ict/mpi/3.1.038/lib64/libmpigf.so.3.2<br>2b3cd258c000-2b3cd258e000 rwxp 0002f000 00:1f 92286590 /apps/intel/ict/mpi/3.1.038/lib64/libmpigf.so.3.2<br>
2b3cd258e000-2b3cd419c000 rwxp 00000000 00:00 0<br>7ffff1d4e000-7ffff1d67000 rwxp 00000000 00:00 0 [stack]<br>7ffff1dff000-7ffff1e00000 r-xp 00000000 00:00 0 [vdso]<br>ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]<br>
Aborted (core dumped)<br></div>
<div>Any clue? Please, help!</div>
<div> </div>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="im"><br>On Tue, Apr 10, 2012 at 10:59 AM, Carsten Kutzner <<a href="mailto:ckutzne@gwdg.de" target="_blank">ckutzne@gwdg.de</a><br></div>
<div class="im"><mailto:<a href="mailto:ckutzne@gwdg.de" target="_blank">ckutzne@gwdg.de</a>>> wrote:<br><br> Hi Steven,<br><br> you might have to remove files with weird names (such as ._name) in<br> the directory where you run<br>
grompp or in your forcefield directory.<br><br> Carsten<br><br><br> On Apr 10, 2012, at 11:52 AM, Steven Neumann wrote:<br><br> > Dear Gmx Users,<br> ><br> > It is 1st time I came across such problem. While preparing my NPT<br>
simulation before umbrella samping:<br> ><br> > grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx<br> -o npt0.tpr<br> ><br> > An input file contains a line longer than 4095 characters, while<br>
the buffer passed to fgets2 has size 4095. The line starts with: '20s'<br> ><br> > Its not about the files in bad format as I have never had this<br> problem - I am using Gromacs 4.5.4 installed on the cluster, I am<br>
using PuTTy shell. I always use dos2gmx ibefore processing.<br> ><br> > Can you advise?<br> ><br> > Steven<br> ><br> > --<br> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
</div> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>
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<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@<u></u>gromacs.org</a>>.
<div class="im"><br> > Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>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>
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<div class="im"><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>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/<u></u>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" target="_blank">gmx-users-request@gromacs.org</a><br></div> <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@<u></u>gromacs.org</a>>.
<div class="im"><br> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br><br><br><br><br></div></blockquote><span class="HOEnZb"><font color="#888888"><br>
<br>-- <br>David van der Spoel, Ph.D., Professor of Biology<br>Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" target="_blank" value="+46184714205">+46184714205</a>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se</a></font></span>
<div class="HOEnZb">
<div class="h5"><br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>Please don'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>
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