[gmx-users] On creating pdb file using dynamic indices from g_select
Hi everyone! I intend to create a trajectory file (in pdb format) of atoms dynamically indexed by g_select. However, I failed to produce the correct pdb file. Here is how I did it. Kindle help please. 1. I created the index file using g_select for water oxygen atoms within 0.4 nm of Atom 3 g_select -f A.xtc -s A.tpr -select 'resname SOL name OW and within 0.4 of atomnr 3' -on X_ndx. The first few lines of X.ndx look like this [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.000 ] [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.200 ] 685 [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.400 ] 685 1045 2. Then I went into trjconv to create a pdb of these water oxygens trjconv -f A.xtc -s A.tpr -o X.pdb -n X.ndx After keying in Enter, I see a list of the the dynamic groups that looks like the ones above. I have 1 groups in the list corresponding to 1 frames but within each frame having different number/indices of water oxygens. I then get a prompt asking me to select a group. I'm not quite sure what number to type but I tried entering 0, 0 to 1, but both gave me wrong pdb files. They dont match with the indices given in X.ndx. How do I tell Gromacs to create a pdb file for these specific atoms? And next time I use a dynamic index, what do I type Gromacs asks to select a group? Thanks.. Sincerely, Bernard -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_msd and MSD analysis
Hi everyone! I have a 20 ns simulation (2fs timestep but coordinates saved every 0.2 ps) and I was able to calculate the mean-square-displacement of the oxygen atoms of my water solvent. The entire MSD plot looks very linear to me. I need to fit this set of MSD data to obtain the diffusion coefficient. However, I am not sure if I will have to use the entire MSD points or may be just to consider a few picoseconds at the latter part of the simulation time. In papers I have read, they use up to a 100 ps, although no mention were made as to where those set of points came from. Please help. This post seems to suggest a nanosecond window for the analysis of the MSD curve http://lists.gromacs.org/pipermail/gmx-users/2012-January/067487.html Although, this other one suggests using the latter 40 ps of his MSD http://lists.gromacs.org/pipermail/gmx-users/2009-November/046990.html Your help is greatly appreciated. Thanks, Bernard-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] H-bonds
Hi everyone! I tried doing H-bond analysis using g_hbond on a solute dissolved in water. The solute has hydroxyl groups. In an attempt to analyze water-bridges formed thru H-bonds, I noticed that g_hbond does not seem to give consistent results. As previously discussed in this list, I am taking advantage of the hbmap file to parse out the Hbond trajectories needed to count the water bridges. A possible water-bridge type is one in which the hydrogen of a water molecule is shared by two different oxygens of the solute. Since there are two H's per water molecule I expected two sets of indices for each H. This is what I did. 1. To simplify parsing the resulting HBMap, I intended to create an HBMap.xpm for a water and a pair of hydroxyl residues from the solute. For a shared H above, that would be (O solute...Hwater...O solute). Creating a set of indices for this configuration was successful upon running (g_hbond -hbn), but only for one set of Hwater. g_hbond was not able to create another set for the other H of water. (Note though that g_hbond was able to correctly identify both Hs of water as donors). g_hbond correctly counted H-bonds for this set and produced a reliable HBMap.xpm 2. Another set of indices was manually created for the other H. However, the hbnum.xvg of this set is unreliable compared with the above and the values shoot to 1000 times expected h-bond counts. Please note that the HBMap.xpm for the hydrogen bonds between water and the solute only lists one H for each water as if ignoring the other H (in cases that there should be two). Your advice/ideas/comments is very much welcome and very much needed. Thanks, Bernard -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] option -r2 on g_hbond, a third HB citerion?
Hi everyone! On this page http://manual.gromacs.org/online/g_hbond.html there is an option -r2 when using g_hbond. What is this r2? I can't find it in the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance which can be switched to H-A by using the -da no. Need help on what is -r2 (could this be for specifying a third criterion for the for distance O-H in addition to the angle cut-off and O-O distance cut-off). Thanks! Bernard -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] On g_hbond
Hi everyone! On this page http://manual.gromacs.org/online/g_hbond.html there is an option -r2 when using g_hbond. What is this r2? I can't find it in the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance which can be switched to H-A by using the -da no. Need help on what is -r2 (could this be for specifying a third criterion for the for distance O-H in addition to the angle cut-off and O-O distance cut-off). Thanks! Bernard-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] CygWin and Gromacs 4.5.5
yes, I have also experience the same with Gromacs 4.5.5 and cygwin. I hope this issue will be addressed.Thanks From: Roland Schulz rol...@utk.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 9, 2011 11:03 AM Subject: Re: [gmx-users] CygWin and Gromacs 4.5.5 On Tue, Nov 8, 2011 at 5:59 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 8/11/2011 11:35 PM, Szilárd Páll wrote: Additionally, AFAIK you will get better performance if you compile with MSVC which should be fairly easy if you use CMake - I'm not entirely sure about this I'd be surprised. Why should MSVC outperform gcc? The file performance is horrible with cygwin (even much slower than a virtual machine). But this should only be important for analysis. For simulation I agree that the performance should be as good (I don't know about NUMA) . Roland Mark though. Cheers, -- Szilárd On Tue, Nov 8, 2011 at 12:41 PM,bh...@udsu.ru wrote: Help me. I want to install Gromacs 4.5.5 with usage CygWin. When I execute a command make I receive the error report: numa_malloc.c:117: error: expected ' ' before ' Processor' numa_malloc.c:117: error: expected ' ' before ' ProcNumber' numa_malloc.c:117: error: expected ' = ', ', ', '; ', ' asm ' or. ... make [3]: *** [numa_malloc.lo] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib/thread_mpi' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src/gmxlib' make [3]: *** [install-recursive] Error 1 make [3]: leaving directory '/cygdrive/. gromacs4.5.5/src' make [3]: *** [install-recursive] Error 1 Where an error? CygWin it is installed with packets: Section Devel - autoconf: Wrapper scripts for autoconf commands - autoconf2.1: Stable version of the automatic configure script builder - autoconf2.5: Development version of the automatic configure script builder - automake1.9: a tool for generating GNU-compliant Makefiles - binutils: The GNU assembler, linker and binary utilites - gcc: A C compiler upgrade helper - gcc-core: A C compiler - gcc-g ++: A C ++ compiler - gcc-g77: Fortran compiler - gcc-mingw-core: Mingw32 support headers and libraries for GCC - gcc-mingw-g ++: Mingw32 support headers and libraries for GCC A C ++ - gcc-mingw-g77: Mingw32 support headers and libraries for GCC Fortran - libgcc1: GCC compiler support shared runtime - libgdbm-devel: GNU dbm database routines (development) - make: The GNU version of the ` make ` utility - mingw-runtime: MinGW Runtime Section Interpreters - perl: Larry Wall ` s Practical Extracting and Report Language Packet FFTW ver.3.2.2 is in addition compiled and installed Trial setting Gromacs of 4.5.3 errors does not give. The instruction on setting took here: http://lists.groma cs.org/pipermail/gmx-users/2009-September/044792.html The error arises only for version Gromacs 4.5.5 Igor -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Gromacs 4.5.5 installation on Cygwin
Hi everyone! I am trying to install Gromacs 4.5.5 using Cygwin. I have succesfully compiled and installed fftw-3.2.2 according to the instructions provided below: http://lists.gromacs.org/pipermail/gmx-users/2009-September/044792.html However, when I am at the step after running make (and after make install, of course), I encounter error messages as follows: numa_malloc.c:117: error: expected '' before 'Processor' numa_malloc.c:117: error: expected '' before 'ProcNumber' numa_malloc.c:117: error: expected '=', ',', ';', 'asm' or . ... ... ... make[3]: ***[numa_malloc.lo] Error 1 make[3]: leaving directory '/cygdrive/.gromacs4.5.5/src/gmxlib/thread_mpi' make[3]: ***[install-recursive] Error 1 make[3]: leaving directory '/cygdrive/.gromacs4.5.5/src/gmxlib' make[3]: ***[install-recursive] Error 1 make[3]: leaving directory '/cygdrive/.gromacs4.5.5/src' make[3]: ***[install-recursive] Error 1 Please help Thanks a lot, Bernard-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Gromacs 4.5.5 installation with Cygwin
Hi everyone! I am trying to install Gromacs 4.5.5 using Cygwin. I have succesfully compiled and installed fftw-3.2.2 according to the instructions provided below. I previously installed a Gromacs-4.5.3 using the same procedure and is still available but as a separate folder. http://lists.gromacs.org/pipermail/gmx-users/2009-September/044792.html However, when I am at the step after running make (and after make install, of course), I encounter error messages as follows: numa_malloc.c:117: error: expected '' before 'Processor' numa_malloc.c:117: error: expected '' before 'ProcNumber' numa_malloc.c:117: error: expected '=', ',', ';', 'asm' or . ... ... ... make[3]: ***[numa_malloc.lo] Error 1 make[3]: leaving directory '/cygdrive/.gromacs4.5.5/src/gmxlib/thread_mpi' make[3]: ***[install-recursive] Error 1 make[3]: leaving directory '/cygdrive/.gromacs4.5.5/src/gmxlib' make[3]: ***[install-recursive] Error 1 make[3]: leaving directory '/cygdrive/.gromacs4.5.5/src' make[3]: ***[install-recursive] Error 1 Please help. Thanks a lot, Bernard-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond
Hi everyone! I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are counted/determined by g_hbond based on angle and distance cut-offs. The distance cut-off is based on the acceptor-donor distance. However, the online manual says that the distance is based on Hydrogen - Acceptor distance? The link to the online manual is as follows: http://manual.gromacs.org/online/g_hbond.html I am using Gromacs 4.5.3. I found out that g_hbond does not give the correct counts due to a bug http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html I am fairly new to using Gromacs with limited knowledge in programming. How do I get this bug fixed with my current version? How can I patch the fix suggested above? The other question will be. Does the most recent version has the g_hbond fixed? I use Gromacs via Cygwin. Just in case I install the the new version, I would like to keep my old one. Is it ok, or do I have remove it? Thanks. Bernard-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond
Hi everyone! I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are counted/determined by g_hbond based on angle and distance cut-offs. The distance cut-off is based on the acceptor-donor distance. However, the online manual says that the distance is based on Hydrogen - Acceptor distance? The link to the online manual is as follows: http://manual.gromacs.org/online/g_hbond.html I am using Gromacs 4.5.3. I found out that g_hbond does not give the correct counts due to a bug http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html I am fairly new to using Gromacs with limited knowledge in programming. How do I get this bug fixed with my current version? How can I patch the fix suggested above? The other question will be. Does the most recent version has the g_hbond fixed? I use Gromacs via Cygwin. Just in case I install the the new version, I would like to keep my old one. Is it ok, or do I have remove it? Thanks. Bernard-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] placing dihedral constraints
Hi Mark and everyone! This has been a previous topic though and thanks Mark for the reply. What I need to do is to calculate the potential energy (energy minimzation) of a molecule at every fixed pairs of dihedrals (phi, psi). I did the suggestions on http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints. In fact what follows is the entry I placed in my topol.top [ dihedral_restraints ] ; ai aj ak al type label phi dphi kfac power 5 1 40 38 1 1 30 0 1 2 12 40 38 34 1 1 10 0 1 2 I also added the following in my mdp file dihre = yes dihre_fc = 1 I removed disre_tau and nstdihreout as they are no longer needed in the recent gromacs versions. Unfortunately, after checking the dihedral angles, they appear to be far from the set value of (phi=30, psi=10). I understand that we are restraining the angles and not constraining/fixing them. Is there a way we can have the resulting phi and psi as close to the required values? I get values 15 degrees away from the original settings. Your help is greatly appreciated. One more question. This restraining will not affect the final potential energy right? Bernard --- On Mon, 6/27/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] placing dihedral constraints To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, June 27, 2011, 5:38 PM On 06/27/2011 07:31 PM, Mr Bernard Ramos wrote: Hi! I would like to freeze two dihedrals/torsion angles but allow the rest (i.e. bonds, angles) to relax during energy minimization and MD. How do I go over applying constraints? Thanks. See http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints to sort out some nomenclature. You probably want a dihedral restraint with a strong force constant (though other approaches are possible). See relevant parts of chapters 4 and 5. Work by analogy from the [dihedrals] and [position_restraints] sections in your existing [moleculetype]. Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] placing dihedral constraints
Thanks, Justin. I'll do experiments on that. Thu, 7/7/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] placing dihedral constraints To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, July 7, 2011, 1:32 AM Mr Bernard Ramos wrote: Hi Mark and everyone! This has been a previous topic though and thanks Mark for the reply. What I need to do is to calculate the potential energy (energy minimzation) of a molecule at every fixed pairs of dihedrals (phi, psi). I did the suggestions on _http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints_. In fact what follows is the entry I placed in my topol.top [ dihedral_restraints ] ; ai aj ak al type label phi dphi kfac power 5 1 40 38 1 1 30 0 1 2 12 40 38 34 1 1 10 0 1 2 I also added the following in my mdp file dihre = yes dihre_fc = 1 I removed disre_tau and nstdihreout as they are no longer needed in the recent gromacs versions. Unfortunately, after checking the dihedral angles, they appear to be far from the set value of (phi=30, psi=10). I understand that we are restraining the angles and not constraining/fixing them. Is there a way we can have the resulting phi and psi as close to the required values? I get values 15 degrees away Increase kfac or dihre_fc. Probably the initial geometry doesn't like the restraint being placed there so you may have to increase the energy penalty for deviating from the restrained value. from the original settings. Your help is greatly appreciated. One more question. This restraining will not affect the final potential energy right? Certainly it will. You'd be preventing (or at the very least, disfavoring) EM from adjusting surrounding coordinates. Such a procedure may have a positive or negative outcome on the final energy. -Justin Bernard --- On *Mon, 6/27/11, Mark Abraham /mark.abra...@anu.edu.au/* wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] placing dihedral constraints To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, June 27, 2011, 5:38 PM On 06/27/2011 07:31 PM, Mr Bernard Ramos wrote: Hi! I would like to freeze two dihedrals/torsion angles but allow the rest (i.e. bonds, angles) to relax during energy minimization and MD. How do I go over applying constraints? Thanks. See http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints to sort out some nomenclature. You probably want a dihedral restraint with a strong force constant (though other approaches are possible). See relevant parts of chapters 4 and 5. Work by analogy from the [dihedrals] and [position_restraints] sections in your existing [moleculetype]. Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 http://us.mc1615.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] On multi-core PCs and gromacs installation
thanks for all the response. I try the suggestions. I think I ll have to do it not with fftw then. --- On Mon, 7/4/11, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: From: Mirco Wahab mirco.wa...@chemie.tu-freiberg.de Subject: Re: [gmx-users] On multi-core PCs and gromacs installation To: gmx-users@gromacs.org Date: Monday, July 4, 2011, 11:08 PM I will be installing gromacs 4.5.x in another computer but this time with four cores. The PC runs in windows and I will be using cygwin. ... Do I still need to install MPI using cygwin? Probably not, but I haven't tested threading on Cygwin. I just did a test for fun and it worked remarkably good, even on Cygwin 1.7 + Win7/x64U box. I'ts very simple using 'make', didn't check cmake (seems more complicated here). The following sequence will lead to success for fully functional Gromacs 4.5.4 for the CYGWIN_i686 target on windows: Install Cygwin 1.7.9 from its page, add + gcc/g++ 4.x and 3.x (but not mingw-gcc variants) + make/cmake + lapack, lapack-devel, lapack-libs + fftw3, *-devel, *-libs + gsl, *-devel, *-libs + wget, tar, vim + bash, rxvt (do not install the 'pthread library stub' entry) Open a cygwin bash shell, create a gromacs base directory and change to it(!): $ mkdir gromacs; cd gromacs Download source and unpack it: $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz $ tar xzf gromacs-4.5.4.tar.gz Write a fancy build control file: $ cat mk_gromacs.sh #!/bin/sh ../gromacs-4.5.4/configure CC=gcc CXX=g++ \ LDFLAGS=-L/usr/lib64 -llapack -lblas -lpthread \ --prefix=/usr/local/gromacs454 \ --with-fft=fftw3 \ --with-external-blas \ --with-external-lapack \ --with-gsl if [ $? -eq 0 ]; then make -j 4 if [ $? -eq 0 ]; then echo echo Success! echo echo now: == make install (as root) / exit fi fi Modify the number in 'make -j 4' to match the number of your processor cores, which is the output of: $ echo $NUMBER_OF_PROCESSORS Create a build directory and change to it(!): $ mkdir build; cd build Run your control script (see above): $ sh ../mk_gromacs.sh Wait and check error messages during configuration (if any), otherwise: go and get a large cup of coffee and lay back. If its ready (without errors), install it by: $ make install Initialize Gromacs environment variables in your shell by modifying your .bashrc file: $ vi .bashrc - go some lines down, at the start of an empty line - press 'i' (insert) - insert the following text # GROMACS if [ -e /usr/local/gromacs454/bin/GMXRC.bash ] ; then source /usr/local/gromacs454/bin/GMXRC.bash fi - press 'Escape' ':' 'x' (to write and close the file) After leaving the shell and opening a new one, mdrun, grommp and friends should be available and working fine. Nothing will do MPI for you. Threading and MPI are complementary approaches to achieving parallelism, and which is better depends on your execution environment. On Cygwin, OpenMPI would't even work anymore as they require MS Visual Studio Library linkage nowadays. One could try MPICH2 which compiled on Cygwin last time I tried (2 years ago?), but why? Gromacs threading works perfectly on Cygwin. Regards M. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] On multi-core PCs and gromacs installation
Hi everyone! I will be installing gromacs 4.5.x in another computer but this time with four cores. The PC runs in windows and I will be using cygwin. The instructions says: If you want to run in parallel across a network, you need MPI. If you are running on a supercomputer you probably already have an optimized MPI version installed - consult your documentation or ask your system administrator. See below for information about how to make use of MPI. As of GROMACS 4.5, threading is supported, so for e.g multi-core workstations, MPI is no longer required The last note says that I do not have to install MPI. Do I still need to install MPI using cygwin? Or cygwin/windows will do the MPI for me. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] placing dihedral constraints
Hi! I would like to freeze two dihedrals/torsion angles but allow the rest (i.e. bonds, angles) to relax during energy minimization and MD. How do I go over applying constraints? Thanks.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] selecting atoms---MD analysis
Hi everyone! I have already have the MD data, I need to select certain atoms/residues with their XYZ coordinates in each time frame. I have problems in using the g_select if this is the proper tool to use for this. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Grompp error on index file
Hi everyone! I added a residue on the gromacs 4.5.3 I have. I followed the instructions as indicated in the Adding A Residue to a Force Field with this link http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue. I added the residue to residuetypes.dat and indicated it as a carbohydrate. The topology in fact was able to write it down as a carbohydrate. Generating a topology went well with pdb2gmx, editconf, genbox, energy minimization. However, I encountered the following error when I was about to do an NVT equilibration. -- Program grompp, VERSION 4.5.3 Source code file: readir.c, line: 1316 Fatal error: Group protein not found in indexfile. Maybe you have non-default groups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n'option. -- In response, I created an index file using make_ndx. The index file was able to generate correctly the molecule indices and identified it correctly as indicated in the residuetypes.dat and carbohydrate.rtp And then I tried (again) the following command: $ grompp -f nvt.mdp -c molecule.gro -n index.ndx -p topol.top -o nvt.tpr. It still generates the same error as above. Please help-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Grompp error on index file
Hi Justin, Thanks for the immediate response. I apologize but I don't have with me the mdp and the top files at the moment. But I will have it e-mailed once I get back to my working gromacs computer. Yes, as I remember, the [moleculetype] at the bottom of the topol.top was able to identify it as a carbohydrate. In fact, the index.file identified it as a carbohydrate. I borrowed the nvt.mdp from the Lysozyme tutorial authored by you. Thanks. --- On Tue, 5/31/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Grompp error on index file To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, May 31, 2011, 10:09 AM Mr Bernard Ramos wrote: Hi everyone! I added a residue on the gromacs 4.5.3 I have. I followed the instructions as indicated in the Adding A Residue to a Force Field with this link _http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue_. I added the residue to residuetypes.dat and indicated it as a carbohydrate. The topology in fact was able to write it down as a carbohydrate. Carbohydrates should be grouped into the other category; I'm not sure Carbohydrate is a recognized type. What do you mean the topology wrote it as a carbohydrate? Is that the [moleculetype] name it was given the topology? __ Generating a topology went well with pdb2gmx, editconf, genbox, energy minimization. However, I encountered the following error when I was about to do an NVT equilibration. -- Program grompp, VERSION 4.5.3 Source code file: readir.c, line: 1316 Fatal error: Group protein not found in indexfile. Maybe you have non-default groups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n'option. -- In response, I created an index file using make_ndx. The index file was able to generate correctly the molecule indices and identified it correctly as indicated in the residuetypes.dat and carbohydrate.rtp Your error does not appear to be connected to the carbohydrate at all. The problem appears to be the use of protein. Capitalization shouldn't matter, so I'm not sure why grompp is complaining. And then I tried (again) the following command: $ grompp -f nvt.mdp -c molecule.gro -n index.ndx -p topol.top -o nvt.tpr. It still generates the same error as above. Please help Please provide your .mdp file and topology, if it is small enough to paste into an email. -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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] On posre.itp
Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] On posre.itp
Thanks for the response. I will be doing a simple MD without the positional restraints. How do I go about reviewing the code for posres? What I did was to add new ff parameters for a new residue I introduced. May I please know what file in the program determines the posres so that I can revew them. Thanks. --- On Sat, 5/7/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] On posre.itp To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, May 7, 2011, 5:10 PM On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote: Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Maybe your atom names are confusing pdb2gmx. Maybe you're comparing apples and oranges with the indices in the coordinate file and the indices in the posres.itp (which are relative to the [atoms], IIRC). Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. Up to you. Do you want to sample under unphysical restraints or not? Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] On posre.itp
I think I've got the answer. It is on the input pdb file. The heavy atoms need to be labeled properly. thanks --- On Sat, 5/7/11, Mr Bernard Ramos bgrquan...@yahoo.com wrote: From: Mr Bernard Ramos bgrquan...@yahoo.com Subject: Re: [gmx-users] On posre.itp To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, May 7, 2011, 5:16 PM Thanks for the response. I will be doing a simple MD without the positional restraints. How do I go about reviewing the code for posres? What I did was to add new ff parameters for a new residue I introduced. May I please know what file in the program determines the posres so that I can revew them. Thanks. --- On Sat, 5/7/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] On posre.itp To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, May 7, 2011, 5:10 PM On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote: Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Maybe your atom names are confusing pdb2gmx. Maybe you're comparing apples and oranges with the indices in the coordinate file and the indices in the posres.itp (which are relative to the [atoms], IIRC). Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. Up to you. Do you want to sample under unphysical restraints or not? Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] RTP file formats
Hi everyone! The *.rtp file formats we have on Gromacs rtp file exmaples do not necessarily have the [dihedrals] or [impropers] part. They normally only have the [atoms] and [bonds]. In fact, the [bonds] section do not enumerate the constants or parameters. This is not what is written or shown as an example in the manual. Is is ok to just enumerate or list down the [atoms] and [bonds] but not including the rest? Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] RTP file formats
Thanks for the response. We will be using the CHARMM ff. --- On Thu, 5/5/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] RTP file formats To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, May 5, 2011, 8:38 PM Mr Bernard Ramos wrote: Hi everyone! The *.rtp file formats we have on Gromacs rtp file exmaples do not necessarily have the [dihedrals] or [impropers] part. They normally only have the [atoms] and [bonds]. In fact, the [bonds] section do not enumerate the constants or parameters. This is not what is written or Different force fields work in different ways. Gromos, for instance, uses #define statements to replace listed gb_*, ga_*, etc. shown as an example in the manual. Is is ok to just enumerate or list The manual shows a generic example, which may not be the same for all force fields. down the [atoms] and [bonds] but not including the rest? Thanks. Per the example in section 5.6.1, only the [bondedtypes] and [atoms] directives are mandatory, but in the case of a bonded molecule, I believe [bonds] are as well. The rest of the directives, if not otherwise specified, are constructed from the existing information. -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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Urey-Bradley constant in CHARMM to GMX
The Urey Bradley constant in CHARMM is expressed in units of kcal per (mol squared angstrom). However, in the Gromacs manual in Table 5.5, it is expressed in kJ/mol. How do we convert the constant from kcal per (mol squared angstrom) to kJ/mol in gromacs. Could gromacs have been expressing this constant in kJ per (mol squared nanometers) rather than in kJ/mol. Thanks, Bernard-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] On dihedral type for CHARMM
Hi everyone! I am currently studying CHARMM ff and I have a question on the functional type of the CHARMM dihedral. On the ffbonded.itp, the function type for CHARMM dihedrals is 9. However, this functional type is not listed on Table 5.5 of the manual. I read that there are 9 supported functional types for dihedrals. Am I correct to assume that func=9is for the CHARMM dihedrals. thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] on force fields
Thanks for the reply on my first querry. I have another one. If I add a NEW atom type in *.atp file, will Gromacs automatically recognize this atom type? Thanks. --- On Wed, 2/16/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] on force fields To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, February 16, 2011, 1:53 PM On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote: Hi everyone! I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010). 1. I will have to change the parameter values in the file ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the only files that I need to update if I need to switch to a new force field? You should make a copy of the whole force field directory into your working directory, rename the new directory suitably, make a suitable change to forcefield.doc, and then edit .itp files suitably. This means you're leaving your reference version untouched and can edit locally to your heart's content, and can be sure you're selecting the right force field with pdb2gmx and/or in your .top file. 2. The new force field 53ACARBO has a new gromos functional form for select torsional potentials. How to I go over implementing this in gromos? Preferably as a sum of existing functional forms. Or use tabulated bonded interactions (see manual and wiki). Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] on force fields
Thank you, sir. That's nice of Gromacs to automatically assign new atom types from an input pdb file. I check out the link as well. --- On Mon, 2/21/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] on force fields To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, February 21, 2011, 10:41 AM Mr Bernard Ramos wrote: Thanks for the reply on my first querry. I have another one. If I add a NEW atom type in *.atp file, will Gromacs automatically recognize this atom type? Theoretically, yes, provided that you supply any corresponding parameters in, e.g., ffnonbonded.itp and ffbonded.itp. However, there is an unresolved bug related to atomtype assignment that may be relevant: http://redmine.gromacs.org/issues/618 It seems to me that any alterations to the .atp file cause things to break down, so do not be surprised if there are problems. -Justin Thanks. --- On *Wed, 2/16/11, Mark Abraham /mark.abra...@anu.edu.au/* wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] on force fields To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, February 16, 2011, 1:53 PM On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote: Hi everyone! I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010). 1. I will have to change the parameter values in the file ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the only files that I need to update if I need to switch to a new force field? You should make a copy of the whole force field directory into your working directory, rename the new directory suitably, make a suitable change to forcefield.doc, and then edit .itp files suitably. This means you're leaving your reference version untouched and can edit locally to your heart's content, and can be sure you're selecting the right force field with pdb2gmx and/or in your .top file. 2. The new force field 53ACARBO has a new gromos functional form for select torsional potentials. How to I go over implementing this in gromos? Preferably as a sum of existing functional forms. Or use tabulated bonded interactions (see manual and wiki). Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] on force fields
Hi everyone! I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010). 1. I will have to change the parameter values in the file ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the only files that I need to update if I need to switch to a new force field? 2. The new force field 53ACARBO has a new gromos functional form for select torsional potentials. How to I go over implementing this in gromos? Thanks. Your help is greatly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] luck
thanks. It was able to generate the needed files as indicated in the tutorial. I trnasfered my working directory. many thanks. Bernard --- On Wed, 2/2/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Gromacs Users' List gmx-users@gromacs.org Date: Wednesday, February 2, 2011, 2:32 AM Mr Bernard Ramos wrote: this is the command i am using: pbd2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce then I choose a force fileld. then I get the error and no new files generated at all. My working directory is: /cygdrive/c/MDProgram/Gromacs453/bin/molecule tests I assume that .../Gromacs453/bin is the location where the Gromacs binaries are installed? It's a bad idea to run commands from the location of the installation or its subdirectories. It's also a possibility that the space in molecule tests is causing problems with filename parsing, but that's a bit of a guess. Move the necessary files to a new location, in a directory named without spaces, and try again. -Justin --- On *Wed, 2/2/11, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, February 2, 2011, 2:15 AM Mr Bernard Ramos wrote: Hi! I am actually following your lysozyme tutorial. I ve been using different pdb files including that of water, methanol, 1AKI, etc. The pdb2gmx does not generate any topology file. No files are generated and I get this error: -- pdb2gmx, VERSION 4.5.3 Source code file: futil.c, line:491 File input/output 1AKI.pdb For more etc -- Then this file doesn't exist in the working directory. What is the command you're issuing (exact copy and paste from the terminal, please)? What are the contents of the working directory? -Justin --- On *Mon, 1/31/11, Mr Bernard Ramos /bgrquan...@yahoo.com http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquan...@yahoo.com/* wrote: From: Mr Bernard Ramos bgrquan...@yahoo.com http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquan...@yahoo.com Subject: Re: [gmx-users] luck To: jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org Date: Monday, January 31, 2011, 1:14 PM thanks. Here is the error i mentioned a while back with using pdb2gmx: -- File input/output error: filename.pdb For more information, visit -- thanks for the time --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu Subject: Re: [gmx-users] luck To: Gromacs Users' List gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:33 PM Mr Bernard Ramos wrote: Do I need to type in g_luck instead? Typing an email and waiting for a response takes far more time and effort than simply trying it yourself ;) -Justin --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two
[gmx-users] luck
Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] luck
Do I need to type in g_luck instead? --- On Mon, 1/31/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? The program is now called g_luck. 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. If the program has given you a fatal error, then the program is correctly installed and working. It is your input that is somehow wrong. Without the actual error message, it's impossible to say what's wrong. -Justin Thanks -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] luck
yup, i typed g_luck and it worked. the error that shows is -- File input/output error: filename.pdb For more information, visit -- --- On Mon, 1/31/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? The program is now called g_luck. 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. If the program has given you a fatal error, then the program is correctly installed and working. It is your input that is somehow wrong. Without the actual error message, it's impossible to say what's wrong. -Justin Thanks -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] luck
thanks. Here is the error i mentioned a while back with using pdb2gmx: -- File input/output error: filename.pdb For more information, visit -- thanks for the time --- On Mon, 1/31/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Gromacs Users' List gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:33 PM Mr Bernard Ramos wrote: Do I need to type in g_luck instead? Typing an email and waiting for a response takes far more time and effort than simply trying it yourself ;) -Justin --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? The program is now called g_luck. 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. If the program has given you a fatal error, then the program is correctly installed and working. It is your input that is somehow wrong. Without the actual error message, it's impossible to say what's wrong. -Justin Thanks -- 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 list gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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 http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Installing Gromacs with Cygwin
Dear all, I need help. I am trying to install Gromacs using Cygwin. However, I do not seem to have access to it. I am very new with Cygwin. I just followed the steps provided by the following sites: http://machine-phase.blogspot.com/2009/04/how-to-install-gromacs-on-windows-vista.html and http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO but in the end when I type luck it returns command not found. These are the steps I did. 1. Downloaded fftw-3.2.2 and gromacs-4.5.3 and saved them in C:\Packages 2. After installing cygwin, I changed directory by typing in the following in order to work with fftw-3.2.2 cd /cygdrive/c/Packages/fftw-3.2.2 and then I typed in ./configure --enable-threads --enable-sse w--enable-float followed by make then make install 2. I then worked for the gromacs-4.5.3 by typing in cd /cygdrive/c/Packages/gromacs-4.5.3 and then ./configure --enable-shared LDFLAGS=-L/usr/local/lib make make install make links make clean 3. I typed luck after all the procedures above but what I get is command not found. I am still at /cygdrivec/Packages/gromacs-4.5.3. Is this the correct path to run the gromacs? Please help. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
