Re: [gmx-users] soft-core and coulomb transformation
bharat v. adkar wrote: Hi David, I am keeping the subject same so that it is helpful to track in future :) On Sat, 10 Nov 2007, David Mobley wrote: Dear Bharat, OK, I went ahead and ran with your topologies using my own run scripts. My runs haven't finished yet, but looking at just values from equilibration, I seem to be seeing roughly the same trends you do. In particular: (1) The forward simulation always gives dv/dlambda values that are fairly close to -2 at each lambda (2) The reverse simulation gives a range of values at different lambda values, and switches from positive to negative as lambda increases. The integral of in the forward case is NOT the negative of the integral of for the reverse case, which is what it should be. Obviously, something is wrong here, and it doesn't seem to be your run input files. I don't see anything obviously wrong with your topology files, either -- as far as I can tell your charge groups are OK. My suggestion is to try to strip this down to a simpler case where it will become more clear what the problem is. Maybe ethane->methane rather than with the capping on the ends. (Did you say you have the same problem with ethane->methane? It would be easier to troubleshoot those topologies). As I mentioned earlier, ethane to methane transformation also shows the same behaviour. I am almost sure that the topologies and other input files are correct. I am pasting below the output of the coulomb-transformation for both, ethane to methane (forward) and methane to ethane (reverse). Topology is the same as i mentioned few mails back... Forward charge transformation lmbd dg/dlerror 0.00 -8.286304 0.0108319 0.05 -8.32708 0.0114018 0.10 -8.328157 0.0095819 0.15 -8.344236 0.00893341 0.25 -8.353463 0.00984712 0.40 -8.368163 0.0104302 0.50 -8.397035 0.00969758 0.60 -8.415603 0.00908416 0.75 -8.448185 0.00941215 0.85 -8.484247 0.00922024 0.90 -8.481465 0.00885981 0.95 -8.495802 0.00961897 1.00 -8.501283 0.00957299 Reverse charge transformation 0.00 13.770658 0.074592 0.05 13.331217 0.0778554 0.10 13.075527 0.0722786 0.15 12.483814 0.0750718 0.25 11.789282 0.0674654 0.40 10.730386 0.0875609 0.50 10.008684 0.0807128 0.60 9.266026 0.0736956 0.75 7.999017 0.0738001 0.85 7.388243 0.0832792 0.90 6.991334 0.0828869 0.95 6.595921 0.0796503 1.00 6.180366 0.0893983 As can be clearly seen, both transformations are not equivalent. (These are output from the 1 ns simulations.) If you get to the point where you're convinced it has nothing to do with your topology, you could submit a bugzilla -- but it would be a good idea to be more sure that there is no problem with your topology, first. Also it would be helpful to have more evidence about where the bug might be, if there is one (hence the importance of stripping this down to the "minimum" topology necessary to reproduce the problem). You might also, for example, just try turning off the charges on methane in water. You could also try turning on the charges in methane in water. These two should be equivalent (except for the sign) of course. Keep me posted on what you find out. to further see what happens, i used cut-off instead of pme and that seems to be giving okay results. i tried running only 20 ps runs as in equilibration, and there the values look as per expectations. then tried with Ace-Ala-Nac <-> Ace-Gly-Nac also. both seems okay. below are the values i obtained: Ethane <-> Methane forward 0.00 -8.277302 0.0747561 0.05 -8.346413 0.105338 0.10 -8.311737 0.0775508 0.15 -8.326182 0.0749244 0.25 -8.383022 0.0741275 0.40 -8.309543 0.199901 0.50 -8.388351 0.0807475 0.60 -8.334778 0.0769525 0.75 -8.444722 0.0556352 0.85 -8.541355 0.0529021 0.90 -8.562161 0.079475 0.95 -8.588182 0.0679287 1.00 -8.535591 0.0505447 reverse 0.00 8.647486 0.0848346 0.05 8.571583 0.067 0.10 8.410289 0.04688 0.15 8.336588 0.085721 0.25 8.536206 0.0457025 0.40 8.452587 0.0730119 0.50 8.397571 0.0540216 0.60 8.379067 0.0775835 0.75 8.345908 0.0889559 0.85 8.408099 0.082048 0.90 8.284268 0.0632315 0.95 8.1428 0.123793 1.00 8.303987 0.0505205 and for Ace-Ala-Nac <-> Ace-Gly-Nac forward 0.00 -2.113457 0.160573 0.05 -2.056746 0.0790143 0.10 -2.619748 0.242052 0.15 -2.470358 0.247365 0.25 -2.121426 0.623961 0.35 -2.210045 0.0567349 0.45 -2.173477 0.0483762 0.50 -2.156053 0.167631 0.55 -2.156565 0.0948302 0.65 -2.194102 0.0810602 0.75 -2.302156 0.306185 0.85 -2.28119 0.0545011 0.90 -1.936869 0.147152 0.95 -2.275215 0.190621 1.00 -2.221756 0.124669 reverse 0.00 2.30627 0.169452 0.05 2.102584 0.181941 0.10 2.531891 0.27292 0.15 2.491334 0.200524 0.25 2.020721 0.0577124 0.35 2.42911 0.133624 0.45 2.113785 0.24776 0.50 2.312891 0.056794 0.55 2.147666 0.0652882 0.65 2.259201 0.0969329 0.75 2.341642 0.0767809 0.85 2.381157 0.19062 0.90 2.29 0.238674 0.95 2.197692 0.175085 1.00 1.921228 0.0853432 in both the cases, the values do not change much, but they appear to be satisfying. So everythings approximatel
Re: [gmx-users] soft-core and coulomb transformation
Hi David, I am keeping the subject same so that it is helpful to track in future :) On Sat, 10 Nov 2007, David Mobley wrote: Dear Bharat, OK, I went ahead and ran with your topologies using my own run scripts. My runs haven't finished yet, but looking at just values from equilibration, I seem to be seeing roughly the same trends you do. In particular: (1) The forward simulation always gives dv/dlambda values that are fairly close to -2 at each lambda (2) The reverse simulation gives a range of values at different lambda values, and switches from positive to negative as lambda increases. The integral of in the forward case is NOT the negative of the integral of for the reverse case, which is what it should be. Obviously, something is wrong here, and it doesn't seem to be your run input files. I don't see anything obviously wrong with your topology files, either -- as far as I can tell your charge groups are OK. My suggestion is to try to strip this down to a simpler case where it will become more clear what the problem is. Maybe ethane->methane rather than with the capping on the ends. (Did you say you have the same problem with ethane->methane? It would be easier to troubleshoot those topologies). As I mentioned earlier, ethane to methane transformation also shows the same behaviour. I am almost sure that the topologies and other input files are correct. I am pasting below the output of the coulomb-transformation for both, ethane to methane (forward) and methane to ethane (reverse). Topology is the same as i mentioned few mails back... Forward charge transformation lmbd dg/dlerror 0.00 -8.286304 0.0108319 0.05 -8.32708 0.0114018 0.10 -8.328157 0.0095819 0.15 -8.344236 0.00893341 0.25 -8.353463 0.00984712 0.40 -8.368163 0.0104302 0.50 -8.397035 0.00969758 0.60 -8.415603 0.00908416 0.75 -8.448185 0.00941215 0.85 -8.484247 0.00922024 0.90 -8.481465 0.00885981 0.95 -8.495802 0.00961897 1.00 -8.501283 0.00957299 Reverse charge transformation 0.00 13.770658 0.074592 0.05 13.331217 0.0778554 0.10 13.075527 0.0722786 0.15 12.483814 0.0750718 0.25 11.789282 0.0674654 0.40 10.730386 0.0875609 0.50 10.008684 0.0807128 0.60 9.266026 0.0736956 0.75 7.999017 0.0738001 0.85 7.388243 0.0832792 0.90 6.991334 0.0828869 0.95 6.595921 0.0796503 1.00 6.180366 0.0893983 As can be clearly seen, both transformations are not equivalent. (These are output from the 1 ns simulations.) If you get to the point where you're convinced it has nothing to do with your topology, you could submit a bugzilla -- but it would be a good idea to be more sure that there is no problem with your topology, first. Also it would be helpful to have more evidence about where the bug might be, if there is one (hence the importance of stripping this down to the "minimum" topology necessary to reproduce the problem). You might also, for example, just try turning off the charges on methane in water. You could also try turning on the charges in methane in water. These two should be equivalent (except for the sign) of course. Keep me posted on what you find out. to further see what happens, i used cut-off instead of pme and that seems to be giving okay results. i tried running only 20 ps runs as in equilibration, and there the values look as per expectations. then tried with Ace-Ala-Nac <-> Ace-Gly-Nac also. both seems okay. below are the values i obtained: Ethane <-> Methane forward 0.00 -8.277302 0.0747561 0.05 -8.346413 0.105338 0.10 -8.311737 0.0775508 0.15 -8.326182 0.0749244 0.25 -8.383022 0.0741275 0.40 -8.309543 0.199901 0.50 -8.388351 0.0807475 0.60 -8.334778 0.0769525 0.75 -8.444722 0.0556352 0.85 -8.541355 0.0529021 0.90 -8.562161 0.079475 0.95 -8.588182 0.0679287 1.00 -8.535591 0.0505447 reverse 0.00 8.647486 0.0848346 0.05 8.571583 0.067 0.10 8.410289 0.04688 0.15 8.336588 0.085721 0.25 8.536206 0.0457025 0.40 8.452587 0.0730119 0.50 8.397571 0.0540216 0.60 8.379067 0.0775835 0.75 8.345908 0.0889559 0.85 8.408099 0.082048 0.90 8.284268 0.0632315 0.95 8.1428 0.123793 1.00 8.303987 0.0505205 and for Ace-Ala-Nac <-> Ace-Gly-Nac forward 0.00 -2.113457 0.160573 0.05 -2.056746 0.0790143 0.10 -2.619748 0.242052 0.15 -2.470358 0.247365 0.25 -2.121426 0.623961 0.35 -2.210045 0.0567349 0.45 -2.173477 0.0483762 0.50 -2.156053 0.167631 0.55 -2.156565 0.0948302 0.65 -2.194102 0.0810602 0.75 -2.302156 0.306185 0.85 -2.28119 0.0545011 0.90 -1.936869 0.147152 0.95 -2.275215 0.190621 1.00 -2.221756 0.124669 reverse 0.00 2.30627 0.169452 0.05 2.102584 0.181941 0.10 2.531891 0.27292 0.15 2.491334 0.200524 0.25 2.020721 0.0577124 0.35 2.42911 0.133624 0.45 2.113785 0.24776 0.50 2.312891 0.056794 0.55 2.147666 0.0652882 0.65 2.259201 0.0969329 0.75 2.341642 0.0767809 0.85 2.381157 0.19062 0.90 2.29 0.238674 0.95 2.197692 0.175085 1.00 1.921228 0.0853432 in both the cases, the values do not change much, but they appear to be satisfying. So everythings approximately zeroes down to the su
Re: [gmx-users] Parallel run on IBM p575 "poe mpi"
liu xin wrote: Hi guys, just a short question, this is how I run a 8np mpi-mdrun job on my machine: poe /home/usr/programs/gromacs331mpi/bin/mdrun -v -s 8np.tpr --procs 8 -nodes 8 -task_per_node 1 -single_thread yes -eager_limit 65535 -shared_memory but it is much slower than the 1np mode, I havent used poe-mpi before, is there something wrong with my options? probably. check your ibm documentation. Yours Xin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] "cannot compute sizeof (int), 77" on AIX 5.3 PPC p575 (searched the list)
hi Christian thx for your reply, I've tried that before with the "--enable-thread" option of fftw, with no success, after I turned it off , the installation seemed OK to me. Yours Xin On Nov 9, 2007 1:21 AM, Christian Burisch <[EMAIL PROTECTED]> wrote: > Hi, > > did you try the solutions given to > http://www.gromacs.org/pipermail/gmx-users/2006-August/023545.html ? > > Regards > > Christian > > > > liu xin schrieb: > > Dear GMXers > > I got the error message " cannot compute sizeof (int)" when I tried to > > configure GMX3.3.1 on IBM PPC p575 AIX5.3, this is how I did it: > > > > for fftw2.1.5 > > export CC="xlc_r -q64 -qhot" > > export CXX="xlC_r -q64 -qhot" > > export OBJECT_MODE=64 > > export FFLAGS="-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1" > > export CFLAGS="-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1" > > ./configure --prefix=/home/usr/programs/fftw215 --enable-float > --enable-mpi > > --enable-thread > > make > > make install > > > > for GMX3.3.1 > > > > export CPPFLAGS=-I/home/usr/programs/fftw215/include > > export LDFLAGS=-I/home/usr/programs/fftw215/lib > > ./configure --prefix=/home/usr/programs/gromacs331mpi --with-fft=fftw2 > > --without-x --disable-fortran --enable-mpi --enable-float > > then I got the following error: > > checking size of int... configure: error: cannot compute sizeof (int), > 77 > > > > have you guys ever experienced this problem before? Any suggestions are > > appreciated! > > > > Yours > > Xin > > > > > > > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > Dr. Christian Burisch > Protein Mechanics and Evolution Group > CAS-MPG Partner Institute for Computational Biology > Shanghai Institutes for Biological Sciences > 320 Yue Yang Road > CN-200031 Shanghai > Tel: +86 21 54920478 > Fax: +86 21 54920451 > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Parallel run on IBM p575 "poe mpi"
Hi guys, just a short question, this is how I run a 8np mpi-mdrun job on my machine: poe /home/usr/programs/gromacs331mpi/bin/mdrun -v -s 8np.tpr --procs 8 -nodes 8 -task_per_node 1 -single_thread yes -eager_limit 65535 -shared_memory but it is much slower than the 1np mode, I havent used poe-mpi before, is there something wrong with my options? Yours Xin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] force=nan in frame 0
dongsheng zhang wrote: Dear Mark, Thank you for your reply. I have used gromacs before. In fact, I have built this FF before, and using it successfully. My old computer was crashed, so I need to do it again. The potential energies looked fine in the md.log. Even I turn off all potentials. I still get the initial foce = nan. Could you please give me any suggest about it? Can't tell. You still haven't told us what you were trying to do when it crashed. EM, MD? Did you minimize and/or equilibrate? Does this installation run other systems? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] force=nan in frame 0
Dear Mark, Thank you for your reply. I have used gromacs before. In fact, I have built this FF before, and using it successfully. My old computer was crashed, so I need to do it again. The potential energies looked fine in the md.log. Even I turn off all potentials. I still get the initial foce = nan. Could you please give me any suggest about it? Thanks! Dongsheng -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Sunday, November 11, 2007 8:40 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] (no subject) dongsheng zhang wrote: > Hello, > > I have build my own FF for a copolomer. When I ran the program, I got > KE > is NaN. I checked the output file trr. I found the initial forces of all > particles at frame 0 are infinite. Could anyone tell me why this > happened? Where I might make a mistake? Thank you in advance! You could have made a mistake at every step. You should do some tutorial material, and get used to the mechanics *before* you attempt to define and use your own forcefields. Learn to walk before trying to run. Check out most of the wiki at http://wiki.gromacs.org Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
dongsheng zhang wrote: Hello, I have build my own FF for a copolomer. When I ran the program, I got KE is NaN. I checked the output file trr. I found the initial forces of all particles at frame 0 are infinite. Could anyone tell me why this happened? Where I might make a mistake? Thank you in advance! You could have made a mistake at every step. You should do some tutorial material, and get used to the mechanics *before* you attempt to define and use your own forcefields. Learn to walk before trying to run. Check out most of the wiki at http://wiki.gromacs.org Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Hello, I have build my own FF for a copolomer. When I ran the program, I got KE is NaN. I checked the output file trr. I found the initial forces of all particles at frame 0 are infinite. Could anyone tell me why this happened? Where I might make a mistake? Thank you in advance! Dongsheng ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re:Re: Incomplete header: nr 3078 time 9408
Dechang Li wrote: >> start by testing the trajectory with gmxcheck > I did what you said. Following is the message: > > Reading frame3000 time 9254.000 Warning at frame 3077. Velocities for > atom 11896 are large (52568.4) > Warning at frame 3077. Velocities for atom 11896 are large (7.68295e+31) > Warning at frame 3077. Velocities for atom 11896 are large (2.75578e+23) > Warning at frame 3077. Velocities for atom 11901 are large (9410) > > WARNING: Incomplete header: nr 3078 time 9408 > > > Item#frames Timestep (ps) > Step 30782 > Time 30782 > Lambda30782 > Coords30782 > Velocities30782 > Forces 0 > Box 30782 > > Did it mean my simulation was failed? But I have checked the energy file > "ener.edr", too. The energy file > seems fine. How did it happen? Can I use the date after time 9254ps? Use gmxcheck on it too... What we're seeing above is that no frames were written after 3078. Either your simulation crashed, or your disk became full. Check your stdout, stderr and .log files for information you've (apparently) missed about this. See http://wiki.gromacs.org/index.php/Doing_Restarts for info about achieving a restart here. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjorder does not write trajectory file
Dmytro Kovalskyy wrote: It works fine for me under 3.3.1 - what command line are you issuing? trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5 Reading the source, both -nshell and -r enforce no trajectory output. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjorder does not write trajectory file
Use the -na and -da flags. trjorder doesn't know how to order the molecules without these. -Justin > Quoting Dmytro Kovalskyy <[EMAIL PROTECTED]>: > > > > It works fine for me under 3.3.1 - what command line are you issuing? > > trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5 > > > > > > -Justin > > > > > > Quoting Dmytro Kovalskyy <[EMAIL PROTECTED]>: > > > > > >> > > >> Trjorder does not write trajectory file, only nshell.xvg > > >> > > >> This is true for 3.3.2 and 3.3.1 versions. > > >> > > >> Dima > > >> > > >> > > >> ___ > > >> gmx-users mailing listgmx-users@gromacs.org > > >> http://www.gromacs.org/mailman/listinfo/gmx-users > > >> Please search the archive at http://www.gromacs.org/search before > > >> posting! > > >> Please don't post (un)subscribe requests to the list. Use the > > >> www interface or send it to [EMAIL PROTECTED] > > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > >> > > > > > > > > > > > > = > > > > > > Justin A. Lemkul > > > Graduate Research Assistant > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > [EMAIL PROTECTED] | (540) 231-9080 > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > > > > = > > > > > > > > > !DSPAM:47367e03304461801161890! > > > > > > > > > > > > > > > > = > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > = = Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:Re: Incomplete header: nr 3078 time 9408
>Send gmx-users mailing list submissions to > gmx-users@gromacs.org > >To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users >or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > >You can reach the person managing the list at > [EMAIL PROTECTED] > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of gmx-users digest..." > > >Today's Topics: > > 1. Re: Incomplete header: nr 3078 time 9408 (David van der Spoel) > 2. Re: trjorder does not write trajectory file (Dmytro Kovalskyy) > > >-- > >Message: 1 >Date: Sun, 11 Nov 2007 09:41:35 +0100 >From: David van der Spoel <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Incomplete header: nr 3078 time 9408 >To: Discussion list for GROMACS users >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=UTF-8; format=flowed > >Dechang Li wrote: >> Dear all, >> >> I used Gromacs-3.3.1 to do a simulation. When it finished, I used >> command "g_dist" to calculate two groups distance VS time. But at time >> 9408ps, it stopped and showed " Incomplete header: nr 3078 time 9408". >> My simulation is 12ns longer. What is the problem? How can I resolve it? >> >> >start by testing the trajectory with gmxcheck I did what you said. Following is the message: Reading frame3000 time 9254.000 Warning at frame 3077. Velocities for atom 11896 are large (52568.4) Warning at frame 3077. Velocities for atom 11896 are large (7.68295e+31) Warning at frame 3077. Velocities for atom 11896 are large (2.75578e+23) Warning at frame 3077. Velocities for atom 11901 are large (9410) WARNING: Incomplete header: nr 3078 time 9408 Item#frames Timestep (ps) Step 30782 Time 30782 Lambda30782 Coords30782 Velocities30782 Forces 0 Box 30782 Did it mean my simulation was failed? But I have checked the energy file "ener.edr", too. The energy file seems fine. How did it happen? Can I use the date after time 9254ps? >> Best regards, >> >> 2007-11-11 >> >> >> = >> Dechang Li, PhD Candidate >> Department of Engineering Mechanics >> Tsinghua University >> Beijing 100084 >> PR China >> >> Tel: +86-10-62773779(O) >> Email: [EMAIL PROTECTED] >> =��� >> >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > >-- >David. > >David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, >Dept. of Cell and Molecular Biology, Uppsala University. >Husargatan 3, Box 596, 75124 Uppsala, Sweden >phone: 46 18 471 4205 fax: 46 18 511 755 >[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > > >-- > >Message: 2 >Date: Sun, 11 Nov 2007 13:01:19 +0200 (EET) >From: "Dmytro Kovalskyy" <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] trjorder does not write trajectory file >To: "Justin A. Lemkul" <[EMAIL PROTECTED]> >Cc: gmx-users@gromacs.org >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain;charset=utf-8 > >> It works fine for me under 3.3.1 - what command line are you issuing? >trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5 >> >> -Justin >> >> Quoting Dmytro Kovalskyy <[EMAIL PROTECTED]>: >> >>> >>> Trjorder does not write trajectory file, only nshell.xvg >>> >>> This is true for 3.3.2 and 3.3.1 versions. >>> >>> Dima >>> >>> >>> ___ >>> gmx-users mailing listgmx-users@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [EMAIL PROTECTED] >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> >> = >> >> Justin A. Lemkul >> Graduate Research Assistant >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> [EMAIL PROTECTED] | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ >> >> ==
Re: [gmx-users] trjorder does not write trajectory file
> It works fine for me under 3.3.1 - what command line are you issuing? trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5 > > -Justin > > Quoting Dmytro Kovalskyy <[EMAIL PROTECTED]>: > >> >> Trjorder does not write trajectory file, only nshell.xvg >> >> This is true for 3.3.2 and 3.3.1 versions. >> >> Dima >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > = > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > = > > > !DSPAM:47367e03304461801161890! > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Incomplete header: nr 3078 time 9408
Dechang Li wrote: Dear all, I used Gromacs-3.3.1 to do a simulation. When it finished, I used command "g_dist" to calculate two groups distance VS time. But at time 9408ps, it stopped and showed " Incomplete header: nr 3078 time 9408". My simulation is 12ns longer. What is the problem? How can I resolve it? start by testing the trajectory with gmxcheck Best regards, 2007-11-11 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Incomplete header: nr 3078 time 9408
Dear all, I used Gromacs-3.3.1 to do a simulation. When it finished, I used command "g_dist" to calculate two groups distance VS time. But at time 9408ps, it stopped and showed " Incomplete header: nr 3078 time 9408". My simulation is 12ns longer. What is the problem? How can I resolve it? Best regards, 2007-11-11 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
