[gmx-users] separation of two strands of DNA during of simulation
Dear Justin thanks for your attention. You said that separation of two strands of DNA during of simulation is a normal consequence of periodic boundary conditions. I had used periodic boundary condition in mdp file as following: Periodic boundary conditions: pbc = xyz Should I delete pbc from mdp file? Whether elimination of pbc prevents separation of two strand of DNA? --- SS -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] separation of two strands of DNA during of simulation
- Original Message - From: shahab shariati shahab.shari...@gmail.com Date: Sunday, May 30, 2010 16:28 Subject: [gmx-users] separation of two strands of DNA during of simulation To: gmx-users@gromacs.org Dear Justin thanks for your attention. You said that separation of two strands of DNA during of simulation is a normal consequence of periodic boundary conditions. I had used periodic boundary condition in mdp file as following: No, he didn't say separation was a consequence of PBC. *Apparent* separation can be. I'm sure he provided this link, but make sure you read it, please :-) http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark Periodic boundary conditions: pbc = xyz Should I delete pbc from mdp file? Whether elimination of pbc prevents separation of two strand of DNA? -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] umbrella sampling
Dear Qian: Debiasing equations for this can be found by analogy to eq. 16 and 17 in the the original Torrie and Valleau US paper: Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling. Alternatively, I used a simple method in doi:10.1016/j.cplett.2008.05.099 which was to run 2-dimensional WHAM with my quantity of interest as the second dimension, but assigning this second dimension a force constant of zero. Be careful with either method, though, as apparent convergence of the free energy does not imply convergence of all other observables. Chris. -- original message -- Hi, I am using Gromacs 4.0.5 for umbrella sampling. I know that I can use g_wham to calculate the free energy along the constrained distance. Is there a command in Gromacs 4.0.5 that can calculates the average of any other obserble (for example, potential energy) along the constrained distance? Thanks a lot. Sincerely, Qian -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] add missing atom
While Mark's answer is entirely complete, I'll just add one more idea in case you don't know where to put the OG. 1. Go into your .gro file and change the SER to an ALA 2. pdb2gmx to place the hydrogens around the CB 3. EM 4a. Copy the EM output .gro file into 3 directories, and in each one of them mutate the ALA back to SER, successively replacing a different HB atom with the OG atom. 4. pdb2gmx to place the hydrogen on the SG 4c. EM 5. Now look at your structures and see if one of them makes any more sense than the others. If you can't tell, then you can run some MD on each and ensure that they interconvert. If it's a really essential SER (like in a binding pocket), you could calculate PMF about chi1. It all depends on how important it is to get the equilibrium location of that OG atom -- and it is at least possible that it is very important (Not only for binding FE calculations, but potentially for conformation: http://www.ncbi.nlm.nih.gov/pubmed/11053148). Chris. -- original message -- I have one question about adding atoms that are missing in residue. This atom is OG in SER amino acid. I don't know how can I add this atom to my residue. If I have to add this atom manually how can I find coordinates of that? Or If there is server or software to do this I will be happy if you suggest me its. There's no automated GROMACS tool, and I haven't used any other particular tool for the task. For just one atom + hydrogen, you're probably fine to guess approximate coordinates and use EM to fix it. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] SPC/E water RDF
Dear Francisco: 1. gromacs already has an spce.itp file. Try using that one directly and see if your answer changes. If it does, then one file is in error. 2. the density of spc/e is not 1g/cc. First thing, you should try to reproduce an RDF from the literature for which you use exactly the same conditions. You mention NPT so try it. Also, be sure that you are using the same cutoffs/PME/etc. 2b. If you can get the published RDF in part 2, then you can try varying one condition at a time, e.g. take your density-equilibrated NPT box and try running some NVT and ensure that you still get the correct RDF. Chris. -- original message -- Dear users, Since I'm new to MD, I coded SPC/E water in the NVT emsemble. Basic ingredients: (1) Number of water molecules N=216 (2) Mass of O = 16 Mass of H = 1 (3) Box density (Periodic Boundary Condition) is exactly 1g/cc (L =18.6205 Angstrom) (4) SPC/E LJ parameters from Berendsen's original 1987 paper (5) Coulomb interaction: Ewald sum Real space ewald: Minimum image convention Ewald convergence parameter for reciprocal sum = 5/L (L is the box length in Ang) Fourier cut-off for ewald reciprocal sum |G| =2*pi*|n|/L, where |n| 27 (6) Nose-Hoover chain NVT (single chain, single thermostat per chain) (7) Time step 1 fs, velocity verlet solver, RATTLE was used to constrain bond lengths and angle, and correct velocities. (8) 100 ps equlibration, 400 ps production (configuration was saved every 25 fs) Everything is fine (energies are stable, etc.) except the second peak in the O-O rdf. The first peak is fine but my second peak seems flat. I find this troubling since all the rdfs I've seen in literature as well the experimental plot have a well-defined second peak. I must mention that in all the papers I've seen the ensemble is NPT (I've not seen NVT yet). In any case, I was expecting my result to match previously published results closely. Can anyone point out what I am doing wrong?? Is NVT not a good ensemble for water simulation?? I'll appreciate it if someone can refer me to a paper that discusses this. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Solvation Free Energy Calculation
Dear Emanuel: We need you to be much more specific. 1. What link? 2. Even though it might be in the link, you should still provide us with a general protocol that you followed. Chris. -- original message -- I am using Gromacs to calculate solvation of free energy calculation. First I tried the tutorial I found on the following link and run all the simulations for different lambda values 36 run for both in water and in vacuum and I got 25215.67 is gromacs calculate this in J or KJ? Even if it in J its way far from the toluene solvation of free energy (-3.1KJ/mol). I got some warnings while I was running the g_analyze which says tau2 is longer than the length of the data (100) invalid fit (statistics might be bad) will fix tau2 at the total time 100, I got this warning for few runs not for all the runs. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mpi-run
Dear GMX Users, I want to run Gromacs on a multiprocessor PC. The MPI files are correctly installed and the gromacs is also configured. However, at the end of configuration section, an Error appears that the FFTW can not be found! Indeed, the FFTW is already installed but the configuration can not locate it! Would you please help me to locate the fftw! Many thanks Mahmoud -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpi-run
nanogroup wrote: Dear GMX Users, I want to run Gromacs on a multiprocessor PC. The MPI files are correctly installed and the gromacs is also configured. However, at the end of configuration section, an Error appears that the FFTW can not be found! Indeed, the FFTW is already installed but the configuration can not locate it! Would you please help me to locate the fftw! Please follow the installation instructions, most notably the information in the Configuration section: http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions#Configuration If you're still having difficulty, please provide more detail, like the actual commands you're issuing, where FFTW is installed, and what the actual error messages are. -Justin Many thanks Mahmoud -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] template.c
Hello all !!
I was playing around with template.c and stuck in a problem.
In the program inside the do loop i.e;
/* This is the main loop over frames */
do {
/* coordinates are available in the vector fr.x
* you can find this and all other structures in
* the types directory under the gromacs include dir.
* Note how flags determines wheter to read x/v/f!
*/
printf (%8.3f\n, fr.time);
if (fr.time == (4000.000 + (50.0 * inc)))
printf (test);
{
for (ra=0; rai;ra++)
{
}
} inc ++;
}while (read_next_frame(status,fr));
The 1st printf statement do prints the frame time. While the 2nd printf
inside the if loop doesnt print any thing, meaning that the if condition is
not being satisfied. I want to execute the statements under if loop after
each 50 ps time.
Can some point out what wrong am I doing.
Thanks
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
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Re: [gmx-users] template.c
On Sun, 2010-05-30 at 21:43 +0530, Chandan Choudhury wrote: Hello all !! I want to execute the statements under if loop after each 50 ps time. I'd just forget any if clauses in the loop and run the program with -dt 50, which gives the same result. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE:Missing atoms
- Original Message - From: you zou zou@live.com Date: Friday, May 28, 2010 14:41 Subject: [gmx-users] add missing atom To: gmx-users@gromacs.org Hi everyone, I have one question about adding atoms that are missing in residue. This atom is OG in SER amino acid. I don't know how can I add this atom to my residue. If I have to add this atom manually how can I find coordinates of that? Or If there is server or software to do this I will be happy if you suggest me its. If there are more than one or two residues or pieces missing, just use O or Pymol to mutate the residues to the same residues, and the saved pdb has all the missing atoms. Then do a quick EM run. Stephan Watkins -- Sicherer, schneller und einfacher. Die aktuellen Internet-Browser - jetzt kostenlos herunterladen! http://portal.gmx.net/de/go/chbrowser -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] template.c
Hi Chandan, The problem is that with floating points the equality in if (fr.time == (4000.000 + (50.0 * inc))) is very unlikely to be satisfied at any time. To compare floating point numbers, you'll have to check whether the value is within a certain interval. But Jussi's approach is far more convenient in this particular case. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 73, Issue 193 (mpi-run)
nanogroup wrote: Dear Justin Many thanks for your response This is the exact phrase: Use CPPFLAGS and LDFLAGS if the library is installed in a non-standard location. (see FAQ at http://www.gromacs.org) If you dont care about performance you can also specify 'fftpack' to use a slower set of FFTs built into Gromacs. (Just install FFTW3 unless you really know what you are doing). But I am realy mixed up by defining the fftw! Without seeing what you're doing, no one can help you. I asked before that you provide the exact commands that you're issuing, as well as a description of what you've installed and where. If you want free help, you have to make it easy for us to help you. The above quote provides useful information, but there's even an example of how to set CPPFLAGS and LDFLAGS on the same page. Also, please do not reply to the entire digest. Cut and paste relevant portions if necessary, and set an appropriate subject line. This helps to avoid a lot of junk in the archive. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] fftw library problem in gromacs installation
Hi , I am having a problem in installing gromacs-4 in a suse linux in a powerpc ibm machine. The problem is that 1. I first installed fftw in the following way :for single precision./configure --enable-float --enable-threads --prefix=/N/u/tg-jmondal/BigRed/UTIL/fftwmakemake install Then for double precisionmake distclean./configure --enable-threads --prefix=/N/u/tg-jmondal/BigRed/UTIL/fftwmakemake install 2. It installed both of them : 3. Now, when I tried to install gromacs4 ./configure --prefix=/N/u/tg-jmondal/BigRed/UTIL/gromacs_mod_4_gcc/ --enable-mpi --program-suffix=mod_4mpi CPPFLAGS=-I/N/u/tg-jmondal/BigRed/UTIL/fftw/include LDFLAGS=-L/N/u/tg-jmondal/BigRed/UTIL/fftw/lib --without-x Here the mpi version is openmpi I get following error:configure: error: Cannot find fftw3f libraryBut, as you may see I have specified the fftw library in configure script So, I went inside config.log file and found the following error: mpicc -o conftest -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -maltivec -mabi=altivec -std=gnu99 -mcpu=7450 -mtune=970 -I/N/u/tg-jmondal/BigRed/UTIL/fftw/include -maltivec -mabi=altivec -L/N/u/tg-jmondal/BigRed/UTIL/fftw/lib conftest.c -lfftw3f -lm 5/usr/bin/ld: skipping incompatible /N/u/tg-jmondal/BigRed/UTIL/fftw/lib/libfftw3f.a when searching for -lfftw3f/usr/bin/ld: cannot find -lfftw3f Looks like there is an incompatibility of mpicc with the fftw library and it may cause some problem. But , I do not know how to resolve this incompatibiilty. Any help will be really appreciated .ThanksJagannath -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] fftw library problem in gromacs installation
- Original Message - From: jagannath mondal jmondal2...@yahoo.co.in Date: Monday, May 31, 2010 5:44 Subject: [gmx-users] fftw library problem in gromacs installation To: gmx-users@gromacs.org Thanks for the detailed post. | Hi , I am having a problem in installing gromacs-4 in a suse linux in a powerpc ibm machine. The problem is that 1. I first installed fftw in the following way : for single precision ./configure --enable-float --enable-threads --prefix=/N/u/tg-jmondal/BigRed/UTIL/fftw make make install Then for double precision make distclean ./configure --enable-threads --prefix=/N/u/tg-jmondal/BigRed/UTIL/fftw make make install 2. It installed both of them : 3. Now, when I tried to install gromacs4 ./configure --prefix=/N/u/tg-jmondal/BigRed/UTIL/gromacs_mod_4_gcc/ --enable-mpi --program-suffix=mod_4mpi CPPFLAGS=-I/N/u/tg-jmondal/BigRed/UTIL/fftw/include LDFLAGS=-L/N/u/tg-jmondal/BigRed/UTIL/fftw/lib --without-x Here the mpi version is openmpi I get following error: configure: error: Cannot find fftw3f library But, as you may see I have specified the fftw library in configure script So, I went inside config.log file and found the following error: mpicc -o conftest -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -maltivec -mabi=altivec -std=gnu99 -mcpu=7450 -mtune=970 -I/N/u/tg-jmondal/BigRed/UTIL/fftw/include -maltivec -mabi=altivec -L/N/u/tg-jmondal/BigRed/UTIL/fftw/lib conftest.c -lfftw3f -lm 5 /usr/bin/ld: skipping incompatible /N/u/tg-jmondal/BigRed/UTIL/fftw/lib/libfftw3f.a when searching for -lfftw3f /usr/bin/ld: cannot find -lfftw3f Looks like there is an incompatibility of mpicc with the fftw library and it may cause some problem. But , I do not know how to resolve this incompatibiilty. Yes. For some reason mpicc (which is normally a wrapper for some other compiler) is finding but not liking the libfftw3f.a. You could try installing FFTW with --enable-shared, in case your linker will only do shared libraries, or something. Alternatively, find out whether the compiler will ever link to static libraries, and if not, probably get a new compiler. The problem could also be with a broken MPI library. Talk to your system admins - this problem looks like it is not specific to GROMACS. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs installation problem in ibm powerpc system
Hi, I am having a problem in a cluster which is IBM PowerPC 970MPs and running SUSE linux and it has IBM XL C Fortran compliers ( xlf, xlc ). I was trying to install gromacs 4 there using open-mpi which is already installed using ibm compilers. Here is my configure command: ./configure --prefix=/N/u/tg-jmondal/BigRed/UTIL/gromacs_mod_4_gcc/ --enable-mpi --program-suffix=mod_4mpi CPPFLAGS=-I/N/soft/linux-sles9-ppc64/fftw3-64-single/include LDFLAGS=-L/N/soft/linux-sles9-ppc64/fftw3-64-single/lib/ --without-x CC=xlc F77=xlf CXX=xlc++ The configuration part went OK. But when I wrote make, it fails with following error: nb_kernel010_ppc_altivec.h, line 42.44: 1506-275 (S) Unexpected text p_nri encountered. nb_kernel010_ppc_altivec.h, line 42.76: 1506-275 (S) Unexpected text iinr encountered. nb_kernel010_ppc_altivec.h, line 42.102: 1506-275 (S) Unexpected text jindex encountered. nb_kernel010_ppc_altivec.h, line 43.70: 1506-275 (S) Unexpected text jjnr encountered. nb_kernel010_ppc_altivec.h, line 43.98: 1506-275 (S) Unexpected text shift encountered. nb_kernel010_ppc_altivec.h, line 43.124: 1506-275 (S) Unexpected text shiftvec encountered. nb_kernel010_ppc_altivec.h, line 44.70: 1506-275 (S) Unexpected text fshift encountered. nb_kernel010_ppc_altivec.h, line 44.98: 1506-275 (S) Unexpected text gid encountered. nb_kernel010_ppc_altivec.h, line 44.124: 1506-275 (S) Unexpected text pos encountered. nb_kernel010_ppc_altivec.h, line 45.70: 1506-275 (S) Unexpected text faction encountered. nb_kernel010_ppc_altivec.h, line 45.98: 1506-275 (S) Unexpected text charge encountered. nb_kernel010_ppc_altivec.h, line 45.123: 1506-275 (S) Unexpected text p_facel encountered. nb_kernel010_ppc_altivec.h, line 46.69: 1506-275 (S) Unexpected text p_krf encountered. nb_kernel010_ppc_altivec.h, line 46.100: 1506-275 (S) Unexpected text p_crf encountered. nb_kernel010_ppc_altivec.h, line 46.130: 1506-275 (S) Unexpected text Vc encountered. nb_kernel010_ppc_altivec.h, line 47.70: 1506-275 (S) Unexpected text type encountered. nb_kernel010_ppc_altivec.h, line 47.96: 1506-275 (S) Unexpected text p_ntype encountered. nb_kernel010_ppc_altivec.h, line 47.126: 1506-275 (S) Unexpected text vdwparam encountered. nb_kernel010_ppc_altivec.h, line 48.70: 1506-275 (S) Unexpected text Vvdw encountered. nb_kernel010_ppc_altivec.h, line 48.97: 1506-275 (S) Unexpected text p_tabscale encountered. make[5]: *** [nb_kernel010_ppc_altivec.lo] Error 1 make[5]: Leaving directory `/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src/gmxlib/nonbonded/nb_kernel_ppc_altivec' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src/gmxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src' make: *** [all-recursive] Error 1 Not sure what it means. Any help to resolve the issue will be highly appreciated. Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
