Re: [gmx-users] final_min_step energy
On 4/07/2011 3:40 PM, balaji nagarajan wrote: Dear Users ! I have a problem in taking the inter and intra molecular interaction energy from a pdb , which is being minimized by minim.mdp ! when i use the g_energy -f *.edr it gives the list of all possible interaction energy as average value , but i want it only for the minimized file how one can fetch that from the *.edr file Check out g_energy -h. There are flags that allow you to choose a subset of the stored values. I'm deliberately not telling you the answer - learn how to look it up and you'll learn other things as well :) 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/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] coiled coil unfolding
Dear Gromacs Users, I am running the simualtions between ligands (10-30) and protein - coiled coil segment. My ligand is strongly hydrophobic and the hydrohpohobic strand between two monomers is obviously hidden. I found that my proetin is unfloding from terminals, two strands open allowing ligands to come into hydrophobic residues - the helical structure is partly destroyed as well as coiled coil. That sounds ok in terms of hydrophobicity. However, maybe I should run simulation with constrained backbone and coiled coil? What do you think? Regards, Jan === Jan Marzinek PhD Candidate Centre for Process Systems Engineering Department of Chemical Engineering Imperial College London South Kensington Campus London SW7 2AZ E: j.marzine...@imperial.ac.ukmailto:j.marzine...@imperial.ac.uk M: +44(0)7411 640 552 -- 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] N-terminus problem
Hi Mark, Thank you for your reply. Let me explain the problem a little more and answer your questions. I would be happy if you could expound upon your reply. Hi Gromacs users, I created a lipopeptide (lauroic acid connected to an 8-residue peptide which starts with Valine). How is the link from acid to peptide created? The link between acid and peptide is a “peptide bond”. (I prepared the *rtp *entry for the lauroic acid make a peptide bond as if lauroic acid was an amino acid (following your suggestion)). If I try to use “pdb2gmx” for ONE LİPOPEPTİDE (9 residues), that is pdb2gmx –f one_lipopeptide.pdb -ter It seems to work. That is, topol.top is created. (And also this topology works for MD.) Does that topology work for MD? Why does pdb2gmx think there's 9 residues, and below there seem to be 63? · But, if I try to use “pdb2gmx” for SEVEN LİPOPEPTİDE at desired positions (63 residues), that is pdb2gmx –f seven_lipopeptide.pdb -ter It gives the fatal error: “Atom N not found in residue seq.nr. 1 while adding improper” While I was creating the lipopeptide, I introduced the lauroic acid as a pseudo amino acid (following Mark’s suggestion). So, I really do NOT have atom N in the first residue. I pasted a part of my gro file below. Some improper in your topology database entries wants a N atom that doesn't exist. Unfortunately, we don't have anywhere near enough information to guess why. pdb2gmx is trying to match your .rtp and specbond entries to your .gro file, but only seeing the latter can't help diagnose a mismatch. Some description of desired positions is also important. I wrote a code to put 7 identical lipopeptides at desired positions. That is, 7 lipopeptides are placed on a plane with 15 degree angle between the adjacent lipopeptides. Also, giving full command lines are always preferred. You may not think anything significant is there, and you might be right, but if there *can* be something significant there, and we aren't given the chance to know whether it is present, we might just not bother to waste time guessing :) I used gromos53a6 force field (extended to include lauroic acid parameters) spc type water And also, I have a question: The first residue in my pdb file is lauroic acid that is DPP, second residue is Valine and so on.. But when I used the pdb2gmx with –ter it says: Start terminus VAL-2: None, End terminus ASP-9: COO-) Would not DPP residue be the start terminus? Best regards, Mark Deniz GROMACS molecule input test 574 1DPP CA1 11.027 5.295 3.153 1DPP CB2 10.894 5.299 3.078 1DPP CG3 10.777 5.234 3.153 1DPP CD4 10.645 5.254 3.078 1DPP CE5 10.521 5.203 3.153 1DPP CZ6 10.392 5.251 3.086 1DPP CM7 10.266 5.207 3.161 1DPP CN8 10.140 5.272 3.103 1DPP CO9 10.014 5.221 3.172 1DPP CP 10 9.885 5.279 3.112 1DPP CQ 11 9.761 5.203 3.160 1DPP C 12 11.101 5.430 3.147 1DPP O 13 11.032 5.531 3.136 2VAL N 14 11.235 5.450 3.160 2VAL H 15 11.249 5.550 3.159 2VAL CA 16 11.368 5.385 3.181 2VAL CB 17 11.390 5.233 3.181 2VALCG1 18 11.332 5.172 3.308 2VALCG2 19 11.338 5.161 3.056 2VAL C 20 11.486 5.449 3.103 2VAL O 21 11.498 5.436 2.982 .. 63ASPOD1 570 -0.306 14.874 3.343 63ASPOD2 571 -0.451 15.030 3.289 63ASP C 572 -0.057 15.023 3.106 63ASP O1 573 0.014 15.003 3.207 63ASP O2 574 -0.029 15.104 3.017 16.23937 16.23937 16.23937 I am using Gromacs 53a6 force field and gromacs 4.5.3 version. Any help will be appreciated. Thanks in advance Deniz -- 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 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] Water-Mediated Hydrogen Bonds
-ins doesn't work as far as I know, and I believe the help text says so. Erik 2 jul 2011 kl. 08.31 skrev Raja Pandian: Dear All, I’m doing research in the field of Protein-DNA interaction. I have gone through these papers, A “Solvated Rotamer” Approach to Modeling Water-Mediated Hydrogen Bonds at Protein–Protein Interfaces “Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study” “Molecular Dynamics Simulation Study of Interaction between Model Rough Hydrophobic Surfaces.” “Prediction of Protein Binding to DNA in the Presence of Water-Mediated Hydrogen Bonds” I have found lot of interesting things on these papers that will be useful for the progress of my research carrier. I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond and water mediated free energy in Gromacs ? Is there any way to calculate water mediated hydrogen bond between Protein-DNA using Gromacs tools? If it is possible, please send your program (water mediated hydrogen bond derivation program) to me and also the program operating procedure. Eagerly waiting for your reply. Thanking You Faithfully Raja -- 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 --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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
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 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] N-terminus problem
On 4/07/2011 11:49 PM, Emine Deniz Tekin wrote: Hi Mark, Thank you for your reply. Let me explain the problem a little more and answer your questions. I would be happy if you could expound upon your reply. Sorry, I can't. * I won't try to make sense of five different font styles and a forest of differential indentation. * You didn't say whether you tested the single lipopeptide topology like I suggested. Solve simple problems completely before tackling complex problems. * I pointed out that showing us only the coordinate file was not an effective way of diagnosing a mismatch of topology database and coordinate file naming, and you still haven't supplied any topology information. * The *geometry* of the lipopetides is often irrelevant for trying to get pdb2gmx to construct a *topology* Mark Hi Gromacs users, I created a lipopeptide (lauroic acid connected to an 8-residue peptide which starts with Valine). How is the link from acid to peptide created? The link between acid and peptide is a “peptide bond”. (I prepared the *rtp *entry for the lauroic acid make a peptide bond as if lauroic acid was an amino acid (following your suggestion)). If I try to use “pdb2gmx” for ONE LİPOPEPTİDE (9 residues), that is pdb2gmx –f one_lipopeptide.pdb -ter It seems to work. That is, topol.top is created. (And also this topology works for MD.) Does that topology work for MD? Why does pdb2gmx think there's 9 residues, and below there seem to be 63? ·But, if I try to use “pdb2gmx” for SEVEN LİPOPEPTİDE at desired positions (63 residues), that is pdb2gmx –f seven_lipopeptide.pdb -ter It gives the fatal error: “Atom N not found in residue seq.nr http://seq.nr/. 1 while adding improper” While I was creating the lipopeptide, I introduced the lauroic acid as a pseudo amino acid (following Mark’s suggestion). So, I really do NOT have atom N in the first residue. I pasted a part of my gro file below. Some improper in your topology database entries wants a N atom that doesn't exist. Unfortunately, we don't have anywhere near enough information to guess why. pdb2gmx is trying to match your .rtp and specbond entries to your .gro file, but only seeing the latter can't help diagnose a mismatch. Some description of desired positions is also important. I wrote a code to put 7 identical lipopeptides at desired positions. That is, 7 lipopeptides are placed on a plane with 15 degree angle between the adjacent lipopeptides. Also, giving full command lines are always preferred. You may not think anything significant is there, and you might be right, but if there *can* be something significant there, and we aren't given the chance to know whether it is present, we might just not bother to waste time guessing :) I used gromos53a6 force field (extended to include lauroic acid parameters) spc type water And also, I have a question: The first residue in my pdb file is lauroic acid that is DPP, second residue is Valine and so on.. But when I used the pdb2gmx with –ter it says: Start terminus VAL-2: None, End terminus ASP-9: COO-) Would not DPP residue be the start terminus? Best regards, Mark Deniz GROMACS molecule input test 574 1DPPCA111.0275.2953.153 1DPPCB210.8945.2993.078 1DPPCG310.7775.2343.153 1DPPCD410.6455.2543.078 1DPPCE510.5215.2033.153 1DPPCZ610.3925.2513.086 1DPPCM710.2665.2073.161 1DPPCN810.1405.2723.103 1DPPCO910.0145.2213.172 1DPPCP109.8855.2793.112 1DPPCQ119.7615.2033.160 1DPPC1211.1015.4303.147 1DPPO1311.0325.5313.136 2VALN1411.2355.4503.160 2VALH1511.2495.5503.159 2VALCA1611.3685.3853.181 2VALCB1711.3905.2333.181 2VALCG11811.3325.1723.308 2VALCG21911.3385.1613.056 2VALC2011.4865.4493.103 2VALO2111.4985.4362.982 .. 63ASPOD1570-0.30614.8743.343 63ASPOD2571-0.45115.0303.289 63ASPC572-0.05715.0233.106 63ASPO15730.01415.0033.207 63ASPO2574-0.02915.1043.017 16.2393716.2393716.23937 I am using Gromacs 53a6 force field and gromacs 4.5.3 version. Any help will be appreciated. Thanks in advance Deniz -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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
[gmx-users] g_mindist on rhombic dodecahedron system
Dear users, following Tsjerk' suggestions, I simulate the protein which had some problems in periodic distance violations in a triclinic box, using instead a rhombic dodecahedron box created with the options: editconf -f prot.gro -o prot_boxdod.gro -bt dodecahedron -d 1.5 -c Minimization, PR-NVT and PR-NPT went OK (no error messages, potential energy after minimization of about -1e+6). I run 30 ns full MD (no PR). At the end of the production MD, I would like to repeat the g_mindist analysis, so I can be sure my system does not suffer again of a periodic distance violation. I performed g_mindist on 4 different systems, and these are my results: 1) on the resulting trajectory: on average, the distance between two periodic distances calculated on the entire protein (option = 1) is 3 nm. However, until 10 ns I can see several spikes going down to 0.1 nm 2) on the resulting trajectory, applying trjconv -pbc nojump before g_mindist: on average, the distance is 0.1 nm 3) on the resulting trajectory, applying trjconv -pbc whole -ur compact before g_mindist: the same as 1) (perfectly superimposable) 4) on the resulting trajectory, applying trjconv -pbc whole -ur compact, then trjconv -pbc nojump, before g_mindist calculation: the same as 2) (perfectly superimposable) My questions are: 1) do I have to transform in some (other) way the trajectory before calculating g_mindist? Do I have to calculate g_mindist in another way (eg. using a different group for calculations)? 2) given these results, can I consider this trajectory suitable for analysis? (maybe excluding the first 10 ns) 3) If not, what can I do more to have a suitable trajectory? Many thanks for any suggestions, I'm quite frustrating for not understanding where the problem comes from... Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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] Water-Mediated Hydrogen Bonds
Hi Raja, You can perform the job calculating h-bond between Protein and Water and between DNA and Water. Now you have to select water that, in the same frame, form h-bond with protein and DNA. The residue information can be found in hbmap.xpm e hbond.log files. There is a perl script in the Justin's webpage (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt) that extract information from this files. You should modify it to reach your goal Francesco Il 04/07/2011 17:02, Erik Marklund ha scritto: -ins doesn't work as far as I know, and I believe the help text says so. Erik 2 jul 2011 kl. 08.31 skrev Raja Pandian: Dear All, I’m doing research in the field of Protein-DNA interaction. I have gone through these papers, *A “Solvated Rotamer” Approach to Modeling Water-Mediated Hydrogen Bonds at Protein–Protein Interfaces* *“Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study”* *“Molecular Dynamics Simulation Study of Interaction between Model Rough Hydrophobic Surfaces.”* *“Prediction of Protein Binding to DNA in the Presence of Water-Mediated Hydrogen Bonds”* I have found lot of interesting things on these papers that will be useful for the progress of my research carrier. I have been looking for water mediated hydrogen bond in my simulation when iuse g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond and water mediated free energy in Gromacs ? Is there any way to calculate water mediated hydrogen bond between Protein-DNA using Gromacs tools? If it is possible, please send your program (water mediated hydrogen bond derivation program) to me and also the program operating procedure. Eagerly waiting for your reply. Thanking You Faithfully Raja -- gmx-users mailing list gmx-users@gromacs.org mailto: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 --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.se mailto:er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Input for n-butanol molecule
Hi, I'm having problem to prepare the archive molecule.itp for n-butanol below, [ moleculetype ] ; name nrexcl BuOH 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 opls_079 1 BuOH HO 1 0.435 2 opls_078 1 BuOH OH 1 -0.700 3 opls_081 1 BuOH CA 1 0.265 4 opls_071 1 BuOH CB 1 0.000 5 opls_071 1 BuOH CC 1 0.000 6 opls_068 1 BuOH CD 1 0.000 [ bonds ] ; ai aj funct c0 c1 1 2 1 0.09450 462750.4 2 3 1 0.13640 376560.0 3 4 1 0.15040 265265.6 4 5 1 0.15040 265265.6 5 6 1 0.15040 265265.6 [ angles ] ; ai aj ak funct c0 c1 4 3 2 1 109.500 418.400 3 2 1 1 108.500 460.240 5 4 3 1 112.700 488.273 6 5 4 1 112.700 488.273 [ dihedrals ] 1 2 3 4 1 0.41840 1.25520 0.0 -1.67360 0.0 0.0 2 3 4 5 1 2.87441 0.58158 2.09200 -5.54799 0.0 0.0 3 4 5 6 1 2.92880 -1.46440 0.20920 -1.67360 0.0 0.0 But I have obtained the following message with the grompp: Fatal error: A non-integer value (2.092000) was supplied for 'multiplicity' in Proper Dih. Thanks for any 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] Input for n-butanol molecule
Juliana Angeiras wrote: Hi, I'm having problem to prepare the archive molecule.itp for n-butanol below, [ moleculetype ] ; name nrexcl BuOH3 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 opls_079 1 BuOH HO 1 0.435 2 opls_078 1 BuOH OH 1 -0.700 3 opls_081 1 BuOH CA 1 0.265 4 opls_071 1 BuOH CB 1 0.000 5 opls_071 1 BuOH CC 1 0.000 6 opls_068 1 BuOH CD 1 0.000 [ bonds ] ; aiaj funct c0 c1 12 1 0.09450 462750.4 23 1 0.13640 376560.0 34 1 0.15040 265265.6 45 1 0.15040 265265.6 56 1 0.15040 265265.6 [ angles ] ; aiajak funct c0c1 4 3 2 1109.500418.400 3 2 1 1108.500460.240 5 4 3 1112.700488.273 6 5 4 1112.700488.273 [ dihedrals ] 1 2 3 4 10.41840 1.25520 0.0 -1.67360 0.0 0.0 2 3 4 5 12.87441 0.58158 2.09200 -5.54799 0.0 0.0 3 4 5 6 12.92880 -1.46440 0.20920 -1.67360 0.0 0.0 But I have obtained the following message with the grompp: Fatal error: A non-integer value (2.092000) was supplied for 'multiplicity' in Proper Dih. The dihedral function type 1 specifies a periodic proper dihedral, which should then list phi, k, and multiplicity. It appears the terms listed are for a Ryckaert-Bellemans dihedral (Cn coefficients), so the type should be changed to 3 instead of 1. -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/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] GMXRC
Hey all, When installing Gromacs 4.5.4 on Windows 7 using Cygwin I ran into an issue involving my computer not having the GMXRC files for me to be able to source them. Any help on this issue? Thanks!! Joe -- 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] GMXRC
On 5/07/2011 10:50 AM, Mr. Joseph S. Castle wrote: Hey all, When installing Gromacs 4.5.4 on Windows 7 using Cygwin I ran into an issue involving my computer not having the GMXRC files for me to be able to source them. Any help on this issue? They were in your source distribution, and should have been installed along with everything else executable. 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/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
Re: [gmx-users] On multi-core PCs and gromacs installation
On 5/07/2011 1:08 AM, Mirco Wahab wrote: 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 Thanks for your detailed instructions, but I would note that this part is not effective - the fftw3 package is compiled in double precision, and your GROMACS install is not. See Cygwin build instructions on the GROMACS webpage. Mark + 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 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
