[gmx-users] PYP Connection
Hi Rama, I was looking at the tdb files for the amber03 force field ( I didn't change anything, i just read with the cat command ), anyways I didn't see anything written in the tdb -n or -c terminal files. After reading the gromacs manual on topology files, it said that residue connection types and such are specified through the tdb file. I'm only guessing that since the chromophore isn't an amino acid that it may have a different connection deviating from the traditional -n or -c terminals. So I was wondering if the amber force field was using the .tdb files that comes standard with gromacs ,... which I'm pretty sure lacks the type of connection that pyp makes with the protein. So to fix this problem, do we need to make or modify the .tdb file for the chromophore, or is the .tdb file of no concern? Thanks, Taylor --- On Wed, 4/20/11, Ramachandran G gtr...@gmail.com wrote: From: Ramachandran G gtr...@gmail.com Subject: Re: [gmx-users] PYP chromophore force field To: Peter C. Lai p...@uab.edu Cc: gmx-users@gromacs.org gmx-users@gromacs.org Date: Wednesday, April 20, 2011, 5:12 PM Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to the Sulphur(S) atom of the Cys-69 residue. But I specified the covalent bond in my topology. [ bonds] C +SG [ angles ] O C +SG CA1 C +SG C +SG +CB [ dihedrals ] O C +SG +CB CA1 C +SG +CB HA2 CA1 C +SG CA2 CA1 C +SG C +SG +CB +CA C +SG +CB +HB1 C +SG +CB +HB2 After doing pdb2gmx, i got the right structure. But the chromophore flies away after minimising. Thanks Rama On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai p...@uab.edu wrote: Isn't the chromophore supposed to be covalently bonded to the protein? My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al 1994 and van Beeumen et al 1993: This small 125-residue protein contains a p-coumaric acid chromophore that is covalently bound to the protein backbone via a thiol-ester cysteine linkage Cys-69... Maybe you forgot to specify a covalent bond in your topology... On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote: Hi gromacs users, I am working on Photo active yellow protein. Although i successfully build the force field and patched the chromophore to the protein. After energy minimizing the protein, the chromophore flies away separately. I don't know whether i am missing anything? Please help. Rama -- 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 -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -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] Re: gmx-users Digest, Vol 84, Issue 177
4. PYP Connection (Taylor Kaplan) Are the connections between the chromophore and cysteine there? You can check this by scanning your topology file for the indices of the sulphur and C1 atom in the [ bonds ] section. You can use the specbond the attach the chromophore to the protein. THis so far always worked for us. hope it helps, Gerrit Message: 4 Date: Thu, 21 Apr 2011 00:48:07 -0700 (PDT) From: Taylor Kaplan taylor_kap...@yahoo.com Subject: [gmx-users] PYP Connection To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 441414.8442...@web36601.mail.mud.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi Rama, I was looking at the tdb files for the amber03 force field ( I didn't change anything, i just read with the cat command ), anyways I didn't see anything written in the tdb -n or -c terminal files. After reading the gromacs manual on topology files, it said that residue connection types and such are specified through the tdb file. I'm only guessing that since the chromophore isn't an amino acid that it may have a different connection deviating from the traditional -n or -c terminals. So I was wondering if the amber force field was using the .tdb files that comes standard with gromacs ,... which I'm pretty sure lacks the type of connection that pyp makes with the protein. So to fix this problem, do we need to make or modify the .tdb file for the chromophore, or is the .tdb file of no concern? Thanks, Taylor --- On Wed, 4/20/11, Ramachandran G gtr...@gmail.com wrote: From: Ramachandran G gtr...@gmail.com Subject: Re: [gmx-users] PYP chromophore force field To: Peter C. Lai p...@uab.edu Cc: gmx-users@gromacs.org gmx-users@gromacs.org Date: Wednesday, April 20, 2011, 5:12 PM Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to the Sulphur(S) atom of the Cys-69 residue. But I specified the covalent bond in my topology. [ bonds] C +SG [ angles ] OC +SG CA1 C +SG C +SG +CB [ dihedrals ] O C +SG+CB CA1C +SG+CB HA2 CA1 C +SG CA2 CA1 C +SG C +SG +CB +CA C +SG +CB +HB1 C +SG +CB +HB2 After doing pdb2gmx, i got the right structure. But the chromophore flies away after minimising. Thanks Rama On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai p...@uab.edu wrote: Isn't the chromophore supposed to be covalently bonded to the protein? My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al 1994 and van Beeumen et al 1993: This small 125-residue protein contains a p-coumaric acid chromophore that is covalently bound to the protein backbone via a thiol-ester cysteine linkage Cys-69... Maybe you forgot to specify a covalent bond in your topology... On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote: Hi gromacs users, I am working on Photo active yellow protein. Although i successfully build the force field and patched the chromophore to the protein. After energy minimizing the protein, the chromophore flies away separately. I don't know whether i am missing anything? Please help. Rama -- 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 -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -Inline Attachment Follows- -- 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 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110421/7c18176f/attachment.html -- -- 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! End
[gmx-users] Improper dihedrals in Charmm FF
Dear all, My molecule contains -CH=CH- fragment and I am trying to create the topology using Charmm FF. It seems that there is no improper dihedrals for -CH=CH- fragment in Charmm FF, while other FF (e.g., Amber or OPLS) has additional improper dihedrals terms for that fragment. Could anybody confirm this? Thanks very much! Cheers, Jianguo-- 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] cholesterol
Hi All, I am new user of gromacs and i want to simulate cholesterol + DOPC as my final year project. firstly i tried gromacs with cholesterol, for which i have downloaded cholesterol pdb and itp file from gromacs site by Monika Hoeltje. i m getting the following error- Residue 'CHOL' not found in residue topology database. I tried PRODRG for generating cholesterol topology file and coordinate file, but still i got the error- invalid directive of atomtype. can someone give me charmm residue topology file for cholesterol or with some solution. Thanks in advance.-- 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] Error compiling Gromacs 4.5.4: relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
Hi all, I have encountered the same problem. With this command: ./configure --with-fft=mkl --prefix=/path/gmx-4.5.3 --enable-mpi make mdrun works well When i used the same option with gmx 4.5.4 ./configure --with-fft=mkl --prefix=/path/gmx-4.5.4 --enable-mpi make mdrun did not work. The compilation reported this error: ld: /usr/local/mpich2-1.3.2p2-install/lib/libmpich.a(allreduce.o): relocation R_X86_64_32 against `_2__STRING.14' can not be used when making a shared object; recompile with -fPIC etc.. the problem here seems to be the use of shared or static libraries. I done configure command several times using the --with-pic and other combinations, however I did not resolve the problem. Perhaps there is an option that I have not seen!! Anyway I released that there is a different default behavior of the configure command. In fact using the options reported above the configure command gives in configure.ac for 4.5.3 at line ~27: AC_DISABLE_SHARED whereas in configure.ac for 4.5.4 ther is AC_ENABLE_SHARED test $enable_mpi = yes AC_DISABLE_SHARED When i changed these two lines in AC_DISABLE_SHARED also gmx4.5.4 is compiled. Luca Pablo Englebienne wrote: Hi all, I'm trying to compile release 4.5.4 on a system that has been running every release since 4.0.4 without a problem. Even 4.5.3 compiled fine with the following configure: LDFLAGS=-L/cvos/shared/apps/fftw/gcc/64/3.2/lib CPPFLAGS=-I/cvos/shared/apps/fftw/gcc/64/3.2/include ./configure --prefix=$HOME/software The LDFLAGS and CPPFLAGS specify the (non-standard) location of the FFTW libraries and headers. Configure succeeds in creating the Makefiles, but when running make it aborts at this point: cc -shared .libs/calcmu.o .libs/calcvir.o .libs/constr.o .libs/coupling.o .libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o .libs/domdec_network.o .libs/domdec_setup.o .libs/domdec_top.o .libs/ebin.o .libs/edsam.o .libs/ewald.o .libs/force.o .libs/forcerec.o .libs/ghat.o .libs/init.o .libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/mvxvf.o .libs/ns.o .libs/nsgrid.o .libs/perf_est.o .libs/genborn.o .libs/genborn_sse2_single.o .libs/genborn_sse2_double.o .libs/genborn_allvsall.o .libs/genborn_allvsall_sse2_single.o .libs/genborn_allvsall_sse2_double.o .libs/gmx_qhop_parm.o .libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o .libs/pme_pp.o .libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o .libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o .libs/stat.o .libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o .libs/vcm.o .libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o .libs/clincs.o .libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o .libs/fft5d.o .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o .libs/qm_gamess.o .libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o .libs/gmx_fft_fftpack.o .libs/gmx_fft_mkl.o .libs/qm_orca.o .libs/mdebin_bar.o -Wl,--rpath -Wl,/home/penglebie/downloads/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath -Wl,/home/penglebie/software/lib /cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a -lxml2 -L/cvos/shared/apps/fftw/gcc/64/3.2/lib ../gmxlib/.libs/libgmx.so -lnsl -lm -msse2 -pthread -Wl,-soname -Wl,libmd.so.6 -o .libs/libmd.so.6.0.0 /usr/bin/ld: /cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a(plan-many-dft-r2c.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 I see that recently (http://lists.gromacs.org/pipermail/gmx-users/2011-April/059919.html) another user encountered the same problem but this time with version 4.5.3; in my case 4.5.3 compiles fine, the only issue is with 4.5.4. The solution is discussed in the installation instructions: http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites The system is running Scientific Linux 5.5. $ uname -a Linux ST-HPC-Main 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux I am puzzled as to why it doesn't work in 4.5.4 but did until the previous release. Did something change in this respect? Maybe, but the fact that this issue has come up numerous times in several versions suggests not. As for why 4.5.3 works and 4.5.4 doesn't, I can't say specifically. Please follow the instructions linked above and see if it fixes your problem. -Justin Regards, Pablo -- gmx-users mailing list
Re: [gmx-users] dna and cnt get distorted in md simulation
majid hasan wrote: Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran molecular dyamics, grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added nsttcouple = -1 value, changed valued of comm_mode from Angular to Linear, changed ns_type value from grid to simple, changed rcoulomb and rvdw values from 0.9 to 1, Both .mdp files are placed at following addresses: http://phas.ubc.ca/~majid/md.mdp (first .mdp file) Is this the file that has had the above modifications made to it for MD? If so, please post the actual file, not the unmodified one. http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file) It seems to me that problem might be related to non-bonded interaction because this is the significant difference between one and two molecule system. Any help would be much appreciated. Why are you employing the free energy code? It seems to me this could be the source of your problems. Each molecule alone is fine, but then by decoupling van der Waals and Coulombic interactions between them, you could be getting instability. Turn off the free energy options and see if you get stable trajectories. -Justin Thanks, Majid -- 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
Re: [gmx-users] cholesterol
On 4/21/2011 8:05 PM, Preeti Gupta wrote: Hi All, I am new user of gromacs and i want to simulate cholesterol + DOPC as my final year project. firstly i tried gromacs with cholesterol, for which i have downloaded cholesterol pdb and itp file from gromacs site by Monika Hoeltje. i m getting the following error- Residue 'CHOL' not found in residue topology database. ... which you need if only if you want to use pdb2gmx on a structure file. I tried PRODRG for generating cholesterol topology file and coordinate file, but still i got the error- invalid directive of atomtype. So you've got some file format wrong... can someone give me charmm residue topology file for cholesterol or with some solution. I think you will profit from doing some tutorial material and looking at the examples in chapter 5 of the manual. 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] temperature effect on potential energy
Hello, I have a quick enquiry whether temperature affects pontetial energy terms. Does T is accounted for to parametrize OPLS FF? Do bonded and nonboded energies vary with T? Thanks, Jennifer N. -- 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] temperature effect on potential energy
On 2011-04-21 15.24, Juliette N. wrote: Hello, I have a quick enquiry whether temperature affects pontetial energy terms. Does T is accounted for to parametrize OPLS FF? Do bonded and nonboded energies vary with T? Have you tried? Try to read up on heat capacity. Thanks, Jennifer N. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] temperature effect on potential energy
I have a quick enquiry whether temperature affects pontetial energy terms. Does T is accounted for to parametrize OPLS FF? Do bonded and nonboded energies vary with T? Have you tried? Try to read up on heat capacity. Hi David, Yes it affects potential. My question is whether this dependence is accounted for in parametrization (k constants in harmonic potentials..) or it affects say nb interactions in the sense that at higher T particles move around faster and it might be that LJ does not attract molecules as it would at lower T. Thanks, Jennifer N. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- Thanks, Jennifer N. -- 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] binding_affinity
Hi Justin Before trying for my system I am trying to learn running these simulation with the help of your tutorial. The only change I made is that I applied pull_code for 2nm movement only in order to save time. Thereafter, with trjconv I generated all 200 conf.gro. when I run your perl script it does gives an oitput of summary_distance.dat. It has one column of conf.gro number but no distance. Where I am wrong. Shahid Nayeem On Tue, Apr 19, 2011 at 6:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin A. Lemkul wrote: shahid nayeem wrote: Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. More of a hybrid of physiological and in vitro conditions. Please see the referenced paper for more details. ...and again, please don't necessarily conclude that just because someone did this for a tutorial that you should inherently be doing it for your system. The tutorial is but one example of a workflow, derived from my own specific work. Construct a model that is most appropriate to your purposes. -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
Re: [gmx-users] binding_affinity
shahid nayeem wrote: Hi Justin Before trying for my system I am trying to learn running these simulation with the help of your tutorial. The only change I made is that I applied pull_code for 2nm movement only in order to save time. Thereafter, with trjconv I generated all 200 conf.gro. when I run your perl script it does gives an oitput of summary_distance.dat. It has one column of conf.gro number but no distance. Where I am wrong. I don't know exactly, but the script runs 500 iterations of each calculation, so you may have 200 lines of content then 300 incomplete lines, unless you've properly modified the script. -Justin Shahid Nayeem On Tue, Apr 19, 2011 at 6:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin A. Lemkul wrote: shahid nayeem wrote: Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. More of a hybrid of physiological and in vitro conditions. Please see the referenced paper for more details. ...and again, please don't necessarily conclude that just because someone did this for a tutorial that you should inherently be doing it for your system. The tutorial is but one example of a workflow, derived from my own specific work. Construct a model that is most appropriate to your purposes. -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 -- 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] Tcoupl default setting
Dear All, I had intended to perform an NPT simulation, however although I selected a barostat I omitted to select a thermostat, nevertheless I did set tc_grps= system, tau_t = 0.1 and ref_t= 300. My temperature appears to fluctuate around the desired 300 K. My question is, by setting tau_t and ref_t has a default thermostat also been turned on by default and if so which one, or have I not performed an NPT but rather an NPE simulation with my apparent well behaved temperature just being coincidental. Needless to say there is no mention of tcoupl in the output file. Regards Charlie. -- 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] Tcoupl default setting
Dear All, I had intended to perform an NPT simulation, however although I selected a barostat I omitted to select a thermostat, nevertheless I did set tc_grps= system, tau_t = 0.1 and ref_t= 300. My temperature appears to fluctuate around the desired 300 K. My question is, by setting tau_t and ref_t has a default thermostat also been turned on by default and if so which one, or have I not performed an NPT but rather an NPE simulation with my apparent well behaved temperature just being coincidental. Needless to say there is no mention of tcoupl in the output file. Regards Charlie. Apologies for possible double posting -- 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] dna and cnt get distorted in md simulation
first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system. In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Thank You, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, April 21, 2011 4:02:57 AM Subject: Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran molecular dyamics, grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added nsttcouple = -1 value, changed valued of comm_mode from Angular to Linear, changed ns_type value from grid to simple, changed rcoulomb and rvdw values from 0.9 to 1, Both .mdp files are placed at following addresses: http://phas.ubc.ca/~majid/md.mdp (first .mdp file) Is this the file that has had the above modifications made to it for MD? If so, please post the actual file, not the unmodified one. http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file) It seems to me that problem might be related to non-bonded interaction because this is the significant difference between one and two molecule system. Any help would be much appreciated. Why are you employing the free energy code? It seems to me this could be the source of your problems. Each molecule alone is fine, but then by decoupling van der Waals and Coulombic interactions between them, you could be getting instability. Turn off the free energy options and see if you get stable trajectories. -Justin Thanks, Majid -- 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 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] dna and cnt get distorted in md simulation
majid hasan wrote: first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system. The reason I asked is that the two are very different - one is for MD and the other is for EM, and in some cases, many of the options are irrelevant for either process so it is somewhat hard to deduce what you're actually trying to accomplish with each, especially given the differences. It is best to only post the actual .mdp files you're using and a description of the output corresponding to each. In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. So, the first .mdp file is the one that actually specifies an MD run, not EM? Or does first correspond to the order of the workflow? It might be best to focus on one process at a time, rather than trying to troubleshoot both EM and MD with some arbitrary designators. CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Bonds don't break or form during classical MD. Any bonds forming or breaking are simply a visualization artifact since you're not reading a topology into the visualization software. From your description, it sounds like these simulations are being conducted in vacuo? I tend to suspect that is the source of the problems. Plain cutoffs for electrostatics lead to nasty artifacts and the presence of a highly charged molecule (DNA) that has no shielding between these charges is quite likely to become very distorted due to its own intrinsic repulsion. -Justin Thank You, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thu, April 21, 2011 4:02:57 AM *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran molecular dyamics, grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added nsttcouple = -1 value, changed valued of comm_mode from Angular to Linear, changed ns_type value from grid to simple, changed rcoulomb and rvdw values from 0.9 to 1, Both .mdp files are placed at following addresses: http://phas.ubc.ca/~majid/md.mdp (first .mdp file) Is this the file that has had the above modifications made to it for MD? If so, please post the actual file, not the unmodified one. http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file) It seems to me that problem might be related to non-bonded interaction because this is the significant difference between one and two molecule system. Any help would be much appreciated. Why are you employing the free energy code? It seems to me this could be the source of your problems. Each molecule alone is fine, but then by decoupling van der Waals and Coulombic interactions between them, you could be getting instability. Turn off the free energy options and see if you get stable trajectories. -Justin Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] dna and cnt get distorted in md simulation
Okay, so here is the file that I used for both energy minimization (with integrator = l-bfgs), and MD (integrator = md). Everything other than the value of integrator was same for both energy minimization and MD. http://phas.ubc.ca/~majid/md.mdp and here is what I see by running .trr files obtained from EM, and MD. On running EM.trr file: In the beginning of simulation, DNA is very stretched i.e atoms of DNA are widely separated from each other, and CNT crumples. Then, gradually DNA shrinks and converges onto CNT. On running MD.trr file: CNT suddenly moves toward and DNA and one part is mixed with DNA and whole structure is crumpled (similar to the final state of EM.trr simulation). Then this crumpled structure wiggles around until the end of simulation. Yes, I ran the whole process in vacuum. I am going to do this simulation by changing cutoff to shift, and see which one works better, and then I will do it with a solvent. Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Thu, April 21, 2011 10:25:35 AM Subject: Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system. The reason I asked is that the two are very different - one is for MD and the other is for EM, and in some cases, many of the options are irrelevant for either process so it is somewhat hard to deduce what you're actually trying to accomplish with each, especially given the differences. It is best to only post the actual .mdp files you're using and a description of the output corresponding to each. In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. So, the first .mdp file is the one that actually specifies an MD run, not EM? Or does first correspond to the order of the workflow? It might be best to focus on one process at a time, rather than trying to troubleshoot both EM and MD with some arbitrary designators. CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Bonds don't break or form during classical MD. Any bonds forming or breaking are simply a visualization artifact since you're not reading a topology into the visualization software. From your description, it sounds like these simulations are being conducted in vacuo? I tend to suspect that is the source of the problems. Plain cutoffs for electrostatics lead to nasty artifacts and the presence of a highly charged molecule (DNA) that has no shielding between these charges is quite likely to become very distorted due to its own intrinsic repulsion. -Justin Thank You, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thu, April 21, 2011 4:02:57 AM *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran molecular dyamics, grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added nsttcouple = -1 value, changed valued of comm_mode from Angular to Linear, changed ns_type value from grid to simple, changed rcoulomb and rvdw values from 0.9 to 1, Both .mdp files are placed at following addresses: http://phas.ubc.ca/~majid/md.mdp (first .mdp file) Is this the file that has had the above modifications made to it for MD? If so, please post the actual file, not the unmodified one.
Re: [gmx-users] dna and cnt get distorted in md simulation
majid hasan wrote: Okay, so here is the file that I used for both energy minimization (with integrator = l-bfgs), and MD (integrator = md). Everything other than the value of integrator was same for both energy minimization and MD. http://phas.ubc.ca/~majid/md.mdp and here is what I see by running .trr files obtained from EM, and MD. On running EM.trr file: In the beginning of simulation, DNA is very stretched i.e atoms of DNA are widely separated from each other, and CNT crumples. Then, gradually DNA shrinks and converges onto CNT. OK, so the DNA is experiencing the charge repulsion I described earlier. The CNT sounds like it does not have proper bonded interactions assigned. On running MD.trr file: CNT suddenly moves toward and DNA and one part is mixed with DNA and whole structure is crumpled (similar to the final state of EM.trr simulation). Then this crumpled structure wiggles around until the end of simulation. If EM is showing such weird results, then you can't really trust anything you see in the MD afterwards. Yes, I ran the whole process in vacuum. I am going to do this simulation by changing cutoff to shift, and see which one works better, and then I will do it with a solvent. There is no point in making this assessment in vacuo and then transferring it to solution. Plain cutoffs should not be used. Their artifacts are well-known and modern simulations should not use them. Shifted functions have discontinuities at their longest cutoff and neglect electrostatic interactions beyond this cutoff. Your best option in solution (especially for highly-charged molecules like DNA) is PME. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Thu, April 21, 2011 10:25:35 AM *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system. The reason I asked is that the two are very different - one is for MD and the other is for EM, and in some cases, many of the options are irrelevant for either process so it is somewhat hard to deduce what you're actually trying to accomplish with each, especially given the differences. It is best to only post the actual .mdp files you're using and a description of the output corresponding to each. In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. So, the first .mdp file is the one that actually specifies an MD run, not EM? Or does first correspond to the order of the workflow? It might be best to focus on one process at a time, rather than trying to troubleshoot both EM and MD with some arbitrary designators. CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Bonds don't break or form during classical MD. Any bonds forming or breaking are simply a visualization artifact since you're not reading a topology into the visualization software. From your description, it sounds like these simulations are being conducted in vacuo? I tend to suspect that is the source of the problems. Plain cutoffs for electrostatics lead to nasty artifacts and the presence of a highly charged molecule (DNA) that has no shielding between these charges is quite likely to become very distorted due to its own intrinsic repulsion. -Justin Thank You, Majid *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Thu, April 21, 2011 4:02:57 AM *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran molecular dyamics, grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted
Re: [gmx-users] dna and cnt get distorted in md simulation
Okay, thank you very much. Sounds very plausibly, I will look up the .itp files for bonded interactions of CNT. Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Thu, April 21, 2011 12:01:46 PM Subject: Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: Okay, so here is the file that I used for both energy minimization (with integrator = l-bfgs), and MD (integrator = md). Everything other than the value of integrator was same for both energy minimization and MD. http://phas.ubc.ca/~majid/md.mdp and here is what I see by running .trr files obtained from EM, and MD. On running EM.trr file: In the beginning of simulation, DNA is very stretched i.e atoms of DNA are widely separated from each other, and CNT crumples. Then, gradually DNA shrinks and converges onto CNT. OK, so the DNA is experiencing the charge repulsion I described earlier. The CNT sounds like it does not have proper bonded interactions assigned. On running MD.trr file: CNT suddenly moves toward and DNA and one part is mixed with DNA and whole structure is crumpled (similar to the final state of EM.trr simulation). Then this crumpled structure wiggles around until the end of simulation. If EM is showing such weird results, then you can't really trust anything you see in the MD afterwards. Yes, I ran the whole process in vacuum. I am going to do this simulation by changing cutoff to shift, and see which one works better, and then I will do it with a solvent. There is no point in making this assessment in vacuo and then transferring it to solution. Plain cutoffs should not be used. Their artifacts are well-known and modern simulations should not use them. Shifted functions have discontinuities at their longest cutoff and neglect electrostatic interactions beyond this cutoff. Your best option in solution (especially for highly-charged molecules like DNA) is PME. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Thu, April 21, 2011 10:25:35 AM *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system. The reason I asked is that the two are very different - one is for MD and the other is for EM, and in some cases, many of the options are irrelevant for either process so it is somewhat hard to deduce what you're actually trying to accomplish with each, especially given the differences. It is best to only post the actual .mdp files you're using and a description of the output corresponding to each. In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. So, the first .mdp file is the one that actually specifies an MD run, not EM? Or does first correspond to the order of the workflow? It might be best to focus on one process at a time, rather than trying to troubleshoot both EM and MD with some arbitrary designators. CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Bonds don't break or form during classical MD. Any bonds forming or breaking are simply a visualization artifact since you're not reading a topology into the visualization software. From your description, it sounds like these simulations are being conducted in vacuo? I tend to suspect that is the source of the problems. Plain cutoffs for electrostatics lead to nasty artifacts and the presence of a highly charged molecule (DNA) that has no shielding between these charges is quite likely to become very distorted due to its own intrinsic repulsion. -Justin Thank You, Majid *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Thu, April 21, 2011 4:02:57 AM *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran
Re: [gmx-users] Error compiling Gromacs 4.5.4: relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
Luca Bellucci wrote: Hi all, I have encountered the same problem. With this command: ./configure --with-fft=mkl --prefix=/path/gmx-4.5.3 --enable-mpi make mdrun works well When i used the same option with gmx 4.5.4 ./configure --with-fft=mkl --prefix=/path/gmx-4.5.4 --enable-mpi make mdrun did not work. The compilation reported this error: ld: /usr/local/mpich2-1.3.2p2-install/lib/libmpich.a(allreduce.o): relocation R_X86_64_32 against `_2__STRING.14' can not be used when making a shared object; recompile with -fPIC etc.. the problem here seems to be the use of shared or static libraries. I done configure command several times using the --with-pic and other combinations, however I did not resolve the problem. Perhaps there is an option that I have not seen!! Anyway I released that there is a different default behavior of the configure command. In fact using the options reported above the configure command gives in configure.ac for 4.5.3 at line ~27: AC_DISABLE_SHARED whereas in configure.ac for 4.5.4 ther is AC_ENABLE_SHARED test $enable_mpi = yes AC_DISABLE_SHARED When i changed these two lines in AC_DISABLE_SHARED also gmx4.5.4 is compiled. I think there may indeed be a problem with the build system, after all. When I checked the configuration output, I saw: ... checking whether to build shared libraries...yes checking whether to build static libraries...yes ... Please file a redmine issue so that this can be investigated, and fixed if necessary. redmine.gromacs.org -Justin Luca Pablo Englebienne wrote: Hi all, I'm trying to compile release 4.5.4 on a system that has been running every release since 4.0.4 without a problem. Even 4.5.3 compiled fine with the following configure: LDFLAGS=-L/cvos/shared/apps/fftw/gcc/64/3.2/lib CPPFLAGS=-I/cvos/shared/apps/fftw/gcc/64/3.2/include ./configure --prefix=$HOME/software The LDFLAGS and CPPFLAGS specify the (non-standard) location of the FFTW libraries and headers. Configure succeeds in creating the Makefiles, but when running make it aborts at this point: cc -shared .libs/calcmu.o .libs/calcvir.o .libs/constr.o .libs/coupling.o .libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o .libs/domdec_network.o .libs/domdec_setup.o .libs/domdec_top.o .libs/ebin.o .libs/edsam.o .libs/ewald.o .libs/force.o .libs/forcerec.o .libs/ghat.o .libs/init.o .libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/mvxvf.o .libs/ns.o .libs/nsgrid.o .libs/perf_est.o .libs/genborn.o .libs/genborn_sse2_single.o .libs/genborn_sse2_double.o .libs/genborn_allvsall.o .libs/genborn_allvsall_sse2_single.o .libs/genborn_allvsall_sse2_double.o .libs/gmx_qhop_parm.o .libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o .libs/pme_pp.o .libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o .libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o .libs/stat.o .libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o .libs/vcm.o .libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o .libs/clincs.o .libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o .libs/fft5d.o .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o .libs/qm_gamess.o .libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o .libs/gmx_fft_fftpack.o .libs/gmx_fft_mkl.o .libs/qm_orca.o .libs/mdebin_bar.o -Wl,--rpath -Wl,/home/penglebie/downloads/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath -Wl,/home/penglebie/software/lib /cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a -lxml2 -L/cvos/shared/apps/fftw/gcc/64/3.2/lib ../gmxlib/.libs/libgmx.so -lnsl -lm -msse2 -pthread -Wl,-soname -Wl,libmd.so.6 -o .libs/libmd.so.6.0.0 /usr/bin/ld: /cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a(plan-many-dft-r2c.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 I see that recently (http://lists.gromacs.org/pipermail/gmx-users/2011-April/059919.html) another user encountered the same problem but this time with version 4.5.3; in my case 4.5.3 compiles fine, the only issue is with 4.5.4. The solution is discussed in the installation instructions: http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites The system is running Scientific Linux 5.5. $ uname -a Linux ST-HPC-Main 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux I am puzzled as to why it doesn't work in 4.5.4 but did until the previous release. Did something change in this respect? Maybe, but the fact that this issue has come up numerous times in
Re: [gmx-users] Tcoupl default setting
On 4/22/2011 1:51 AM, Charlie Forde wrote: Dear All, I had intended to perform an NPT simulation, however although I selected a barostat I omitted to select a thermostat, nevertheless I did set tc_grps= system, tau_t = 0.1 and ref_t= 300. My temperature appears to fluctuate around the desired 300 K. My question is, by setting tau_t and ref_t has a default thermostat also been turned on by default No. and if so which one, or have I not performed an NPT but rather an NPE simulation with my apparent well behaved temperature just being coincidental. Needless to say there is no mention of tcoupl in the output file. Generate a short run that does use temperature coupling and compare the .log files with diff. Or, just read through the first few hundred lines of your .log file to see what it (doesn't) report about T-coupling. 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] temperature effect on potential energy
On 4/21/2011 11:37 PM, Juliette N. wrote: I have a quick enquiry whether temperature affects pontetial energy terms. Does T is accounted for to parametrize OPLS FF? Do bonded and nonboded energies vary with T? Have you tried? Try to read up on heat capacity. Hi David, Yes it affects potential. My question is whether this dependence is accounted for in parametrization (k constants in harmonic potentials..) The generated parameters have no explicit T-dependence, so the functions in which they appear do not have T-dependence either. If you want to know how a force field was parametrized, then there's no substitute for getting the literature and reading it. or it affects say nb interactions in the sense that at higher T particles move around faster and it might be that LJ does not attract molecules as it would at lower T. AFAIK, the physical interactions modelled by the LJ potential are not dependent on particle velocities, so why should the LJ not attract molecules at higher T? Something moving faster doesn't mean it's less attracted to things that it would be attracted to when traveling slower... gravity doesn't magically suspend for an aeroplane... Mark Thanks, Jennifer N. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 -- Thanks, Jennifer N. -- 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] Improper dihedrals in Charmm FF
On 4/21/2011 6:54 PM, Jianguo Li wrote: Dear all, My molecule contains -CH=CH- fragment and I am trying to create the topology using Charmm FF. It seems that there is no improper dihedrals for -CH=CH- fragment in Charmm FF, while other FF (e.g., Amber or OPLS) has additional improper dihedrals terms for that fragment. Could anybody confirm this? That seems to be the case, but you should go and look at the primary sources (CHARMM parameter files and literature) to see what reasoning might exist. 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] grompp error
Hello, I am trying to run a simulation for flexiable water. I use the parameters from J. Chem. Phys. (2006),124,024503 paper and made a spc_fw.itp file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_116 OW 8 9.95140-0.820 A3.165492e-01 6.50299455e-01 opls_117 HW 1 4.03200 0.410 A0.0e+00 0.0e+00 [ bondtypes ] ; ij func b0 kb OWHW 11.012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HW OW HW 1 113.24317.5656 ; J. Chem. Phys. (2006),124,024503 I am geting the error for grompp -f minim.mdp -c water.pdb -p water.top -o 1.tpr error I am getting rogram grompp, VERSION 4.0.7 Source code file: topio.c, line: 415 Fatal error: Syntax error - File water.top, line 26 Last line read: '[ system ]' Invalid order for directive system How can I fix this error? Nilesh -- 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
Nilesh Dhumal wrote: Hello, I am trying to run a simulation for flexiable water. I use the parameters from J. Chem. Phys. (2006),124,024503 paper and made a spc_fw.itp file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_116 OW 8 9.95140-0.820 A3.165492e-01 6.50299455e-01 opls_117 HW 1 4.03200 0.410 A0.0e+00 0.0e+00 [ bondtypes ] ; ij func b0 kb OWHW 11.012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HW OW HW 1 113.24317.5656 ; J. Chem. Phys. (2006),124,024503 I am geting the error for grompp -f minim.mdp -c water.pdb -p water.top -o 1.tpr error I am getting rogram grompp, VERSION 4.0.7 Source code file: topio.c, line: 415 Fatal error: Syntax error - File water.top, line 26 Last line read: '[ system ]' Invalid order for directive system How can I fix this error? Assemble the components of your .top in the correct order, as described in chapter 5 of the manual. Without seeing the contents of water.top that's the best anyone can offer. -Justin Nilesh -- 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
Re: [gmx-users] grompp error
Thanks Justin, Here I pasted water.top ; ; File 'water.top' was generated ; By user: ndhumal (36026) ; On host: c63 ; At date: Thu Apr 21 14:52:38 2011 ; ; This is your topology file ; Protein ; ; Include forcefield parameters #include ffoplsaa.itp ; Include water topology ;#include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions ;#include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols SOL 256 Nilesh On Thu, April 21, 2011 8:03 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to run a simulation for flexiable water. I use the parameters from J. Chem. Phys. (2006),124,024503 paper and made a spc_fw.itp file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_116 OW 8 9.95140-0.820 A3.165492e-01 6.50299455e-01 opls_117 HW 1 4.03200 0.410 A0.0e+00 0.0e+00 [ bondtypes ] ; ij func b0 kb OWHW 11.012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HW OW HW 1 113.24317.5656 ; J. Chem. Phys. (2006),124,024503 I am geting the error for grompp -f minim.mdp -c water.pdb -p water.top -o 1.tpr error I am getting rogram grompp, VERSION 4.0.7 Source code file: topio.c, line: 415 Fatal error: Syntax error - File water.top, line 26 Last line read: '[ system ]' Invalid order for directive system How can I fix this error? Assemble the components of your .top in the correct order, as described in chapter 5 of the manual. Without seeing the contents of water.top that's the best anyone can offer. -Justin Nilesh -- 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 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
Nilesh Dhumal wrote: Thanks Justin, Here I pasted water.top ; ; File 'water.top' was generated ; By user: ndhumal (36026) ; On host: c63 ; At date: Thu Apr 21 14:52:38 2011 ; ; This is your topology file ; Protein ; ; Include forcefield parameters #include ffoplsaa.itp ; Include water topology ;#include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions ;#include ions.itp Up to this point, you haven't defined any molecules. You've commented out every topology and applied a [position_restraints] directive to a non-existent moleculetype. So you've defined a force field, and then a system for which no molecules exist, hence the error. -Justin [ system ] ; Name Protein [ molecules ] ; Compound#mols SOL 256 Nilesh On Thu, April 21, 2011 8:03 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, I am trying to run a simulation for flexiable water. I use the parameters from J. Chem. Phys. (2006),124,024503 paper and made a spc_fw.itp file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_116 OW 8 9.95140-0.820 A3.165492e-01 6.50299455e-01 opls_117 HW 1 4.03200 0.410 A0.0e+00 0.0e+00 [ bondtypes ] ; ij func b0 kb OWHW 11.012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HW OW HW 1 113.24317.5656 ; J. Chem. Phys. (2006),124,024503 I am geting the error for grompp -f minim.mdp -c water.pdb -p water.top -o 1.tpr error I am getting rogram grompp, VERSION 4.0.7 Source code file: topio.c, line: 415 Fatal error: Syntax error - File water.top, line 26 Last line read: '[ system ]' Invalid order for directive system How can I fix this error? Assemble the components of your .top in the correct order, as described in chapter 5 of the manual. Without seeing the contents of water.top that's the best anyone can offer. -Justin Nilesh -- 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 -- 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
