Re: [gmx-users] How to add a repulsive harmonic potential
Depending on how structurally complex the ligands are, it may be very easy to define a dummy atom within the structure using a virtual site, then specifying a nonbonded interaction only between these virtual sites using [nonbond_params]. That way, these sites will not affect ligand-water, ligand-protein, etc but will repel ligands from one another. Thanks for your reply. I tried to use [virtual_sitesn] and [nonbond_params] below. VS1 means virtual site( dummy atoms) of center of mass of one ligand_1. VS2 means virtual site( dummy atoms) of center of mass of one ligand_2. Complex.top file [atomtypes] ;name bond_type mass charge ptype sigmaepsilon . VS1 VS10. 0. V 0.0e+00 0.0e+00 VS2 VS20. 0. V 0.0e+00 0.0e+00 [ nonbond_params ] ;i j func V(c6)W(c12) VS1 VS2 1 0.0e+00 5.8954e+03 [atoms] ;nrtype resnr residue atom cgnr charge mass . 100 ha 2 LIGH71000.211321.0 101 VS13 VIRVS1 1010.00.0 102 VS24 VIRVS2 1020.00.0 [ virtual_sitesn ] ; Site funct from 1012 25 26 27 28 1022 75 76 77 78 However, I got fatal error below. Fatal error: Number of coordinates in coordinate file(NVT_1.gro, 77111) Does not match topology (complex.top, 77113) Does it mean that I have to add coordinate information of dummy atoms(VS1, VS2) in .gro file ? Or is how to define virtual site incorrect? Best regards, Atsutoshi Okabe Thank you for your help. Actually, I want to predict the binding mode of ligand for protein/ligand complex during long time simulation, so I want to add only repulsive potential between ligands to avoid ligand aggregation, not fix these ligands. The reason why I add some ligand molecules(not one ligand) in simulation is to enhance ligand sampling. I tried using [distance_restaints] below, not use [bonds] because of domain decomposition error. Then, the MD simulation could run normally without domain decomposition error! [ distance_restraints ] ;ai aj type index type' low up1 up2 fac 13 63 11 120 100 100 1 However, the distance between 13 atom and 63 atom seems to be less than 20 angstrom in every steps of MD simulation. So I tried to change the fac value from 1 to -1, but the distance was less than 20 angstrom during MD simulation Why the ligands were restrained less than 20 angstrom although I think I add repulsive force between these atoms? Depending on how structurally complex the ligands are, it may be very easy to define a dummy atom within the structure using a virtual site, then specifying a nonbonded interaction only between these virtual sites using [nonbond_params]. That way, these sites will not affect ligand-water, ligand-protein, etc but will repel ligands from one another. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to call an external LAPACK function in gromacs
Hi, When you ran cmake originally, what did it report about which LAPACK it found and will use? (You may need to clean your build tree and start again in order to find this out.) What is the linker command line now (e.g. make VERBOSE=1) Mark On Mon, Apr 13, 2015 at 11:30 PM, qian wang qq.wang...@gmail.com wrote: Dear All, I am a new user of gromacs 5.0. For my own purposes I made small changes in a gromacs source code where I called a function named DPOTRF. This is a standard function in LAPACK library but not in the gromacs internal LAPACK library. Now I have a problem of compiling. What I did is: cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DCMAKE_PREFIX_PATH=/usr/lib64 (this is the path of my extenal LAPACK library) this step is ok but next when I make, the error I got is: Linking CXX executable ../../bin/template ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 Could anyone help me with this problem? Thanks a lot. Sincerely, Qian -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Print Charmm27 parameters
Hi, On Sat, Apr 11, 2015 at 1:06 PM, Stavros Chatzieleftheriou stavros...@windowslive.com wrote: Dear all, I am new to Gromacs and I have a simple question. How can I get the exact force field parameters used for my .pdb file (i.e. kb and bo for bonded terms, kth and tho for angle terms e.t.c.) from Gromacs ? These are all looked up from the database for each force field. Manual chapter 5 talks about how all this machinery works. Mark At the topol .itp file I can see the connectivity between the atoms but not the rest of the information I need. Is there a specific command that I should type? Thanks in advance, Stavros ChatzieleftheriouPhD Candidate at the National Technical University of Athens -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] adding SR2++ to charm27 force field
Hi Mark, Thanks for your reply. I am sure as I changed the files in the charmm27.ff installed in my unbuntu system. Is there any other things I need to consider? Thanks, Ming -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: Tuesday, 14 April 2015 6:53 PM To: Discussion list for GROMACS users Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] adding SR2++ to charm27 force field Hi, Inspect the whole output. Is pdb2gmx picking up the version of charmm27 you think it is? Mark On Tue, Apr 14, 2015 at 8:40 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, I am trying to add SR 2++ in charm27 force field. I modified the ffnonbonded.itp, ffnanonbonded.itp, ions.itp, aminoacids,rtp, atomtypes.atp according to the parameters of SR in oplsaa.ff. However, when using pdb2gmx, I came across the following fatal error: Atomtype SR not found. Could anybody give me some advice? Thanks in advance, Ming -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Number of hardware threads does not match OpenMP
On Tue, Apr 14, 2015 at 8:58 AM, Dries Van Rompaey dries.vanromp...@gmail.com wrote: Dear Szilárd, Thanks for your reply. I'll try your proposed fix. I was also wondering if the simulations performed could be affected in terms of reliability and accuracy or not (ie. do I need to redo the simulations already performed with the corrected settings)? No, they're correct. Only efficiency is in question. Mark Thanks! Dries -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Post-Processing on the REMD trj
On Tue, Apr 14, 2015 at 2:50 AM, 14110220...@fudan.edu.cn 14110220...@fudan.edu.cn wrote: Dear users, Rescently, I used REMD to do some simulation by Gromacs , I konw GROMACS exchanges coordinates. So does this means every trajectory was written at a temperture ?AND if i want to analyse the lowest temperature, can I just analyse md0.xtc as 'trajectory no longer be continuous'( http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations:_Mark_Abraham,_Session_1B )? Yes. In REMD trajectories, you must choose whether you want a continuous trajectory or a continuous ensemble. mdrun writes the latter. secondly， the Perl script demux.pl can analyse a single REMD .log file and writes two special .xvg files .But i got some problem ,as we can see blow , 0 0 1 2 3 4 5 6 7 8 4 0 1 2 3 4 5 6 7 8 8 0 1 2 3 4 5 6 8 7 12 012435687 16 012435687 20 012436587 24 021435678 28 021435678 32 021435678 36 021435678 40 021435678 44 021345678 48 021345678 52 012435678 56 012435678 60 021345678 64 012345687 68 012345687 72 012345687 76 012345687 the 0 didn't exchange ,however the log describes the 0 did exchange . When? And when did it exchange back? And how do those compare to the time stamps in the left-hand column? There's nothing to demux if there had been no net exchange on replica 0 by the time output was written. Mark i think my log produced by gromacs4.6.5 doesn't match the Perl script demux.pl. Can someone tell me how to modify the Perl script demux.pl.? thank you Dongdong Wang -- Dongdong Wang Chemistry Department Fudan University 200433, Shanghai P.R. China Tel:+86 15121115863 Email: 14110220...@fudan.edu.cn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Position restraint for ions
Hi! I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group non-Water'* - to create an index for my RNA and Ions; and: *genrestr -f rna_ions.gro -n rna_ion.ndx -o rna_ion.itp -fc 800 800 800* - to create an .itp file for them. I am also including this new .itp file to the topology using the proper 'ifdef' statements, but I get this when I run grompp: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? Cheers! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to add a repulsive harmonic potential
On 4/14/15 3:13 AM, atsutoshi.ok...@takeda.com wrote: Depending on how structurally complex the ligands are, it may be very easy to define a dummy atom within the structure using a virtual site, then specifying a nonbonded interaction only between these virtual sites using [nonbond_params]. That way, these sites will not affect ligand-water, ligand-protein, etc but will repel ligands from one another. Thanks for your reply. I tried to use [virtual_sitesn] and [nonbond_params] below. VS1 means virtual site( dummy atoms) of center of mass of one ligand_1. VS2 means virtual site( dummy atoms) of center of mass of one ligand_2. Complex.top file [atomtypes] ;name bond_type mass charge ptype sigmaepsilon . VS1 VS10. 0. V 0.0e+00 0.0e+00 VS2 VS20. 0. V 0.0e+00 0.0e+00 [ nonbond_params ] ;i j func V(c6)W(c12) VS1 VS2 1 0.0e+00 5.8954e+03 This isn't mathematically consistent, nor do I think it will be stable. That is a massive repulsion at just about any distance. For a bit gentler approach, please consider what we do with hydrophobic fragments here: http://pubs.acs.org/doi/abs/10.1021/ci100462t [atoms] ;nrtype resnr residue atom cgnr charge mass . 100 ha 2 LIGH71000.211321.0 101 VS13 VIRVS1 1010.00.0 102 VS24 VIRVS2 1020.00.0 [ virtual_sitesn ] ; Site funct from 1012 25 26 27 28 1022 75 76 77 78 However, I got fatal error below. Fatal error: Number of coordinates in coordinate file(NVT_1.gro, 77111) Does not match topology (complex.top, 77113) Does it mean that I have to add coordinate information of dummy atoms(VS1, VS2) in .gro file ? All particles require coordinates. They're virtual, but they're not magical. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to call an external LAPACK function in gromacs
Hi, On Tue, Apr 14, 2015 at 4:15 PM, qian wang qq.wang...@gmail.com wrote: Hi, Here is the information. Thank you. cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DCMAKE_PREFIX_PATH=/usr/lib64: Looking for sgemm_ -- Looking for sgemm_ - found -- A library with BLAS API found. -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Found the ability to use plug-ins when building shared libaries, so will compile to use plug-ins (e.g. to read VMD-supported file formats) . Configuring done OK, it did find your LAPACK. make . Linking CXX executable ../../bin/template /usr/bin/c++-march=core-avx2 -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -rdynamic ../../lib/libgromacs.so.0.0.0 -fopenmp -ldl -lrt -lm -lfftw3f -lblas -llapack -lblas -llapack -lpthread -Wl,-rpath,/home/qw9/Downloads/gromacs-5.0/build/lib ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 That works for me (i.e. the linker line has system BLAS and LAPACK libraries). Please try the latest 5.0.4 release, we might well have fixed a bug in the template compilation stuff. In any case, in 5.0.x the intended use case for the template is to install GROMACS, and then copy the installed template machinery somewhere so you can use it. Even then, per the README you will find in share/template, you will might have to teach CMake that it should augment the linking path. Mark Sincerely, Qian On Tue, Apr 14, 2015 at 3:56 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, When you ran cmake originally, what did it report about which LAPACK it found and will use? (You may need to clean your build tree and start again in order to find this out.) What is the linker command line now (e.g. make VERBOSE=1) Mark On Mon, Apr 13, 2015 at 11:30 PM, qian wang qq.wang...@gmail.com wrote: Dear All, I am a new user of gromacs 5.0. For my own purposes I made small changes in a gromacs source code where I called a function named DPOTRF. This is a standard function in LAPACK library but not in the gromacs internal LAPACK library. Now I have a problem of compiling. What I did is: cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DCMAKE_PREFIX_PATH=/usr/lib64 (this is the path of my extenal LAPACK library) this step is ok but next when I make, the error I got is: Linking CXX executable ../../bin/template ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 Could anyone help me with this problem? Thanks a lot. Sincerely, Qian -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Position restraint for ions
On 4/14/15 1:48 PM, Marcelo Depólo wrote: Hi! I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group non-Water'* - to create an index for my RNA and Ions; and: *genrestr -f rna_ions.gro -n rna_ion.ndx -o rna_ion.itp -fc 800 800 800* - to create an .itp file for them. I am also including this new .itp file to the topology using the proper 'ifdef' statements, but I get this when I run grompp: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] adding SR2++ to charm27 force field
On Tue, Apr 14, 2015 at 11:12 AM, Ming Tang m21.t...@qut.edu.au wrote: Hi Mark, Thanks for your reply. I am sure as I changed the files in the charmm27.ff installed in my unbuntu system. Is there any other things I need to consider? pdb2gmx lists the full path to the folder in which it finds the files it is actually using. The most likely problem is that it's not finding what you think it is, and there are many and frequent ways that could happen. Please check that. Mark Thanks, Ming -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: Tuesday, 14 April 2015 6:53 PM To: Discussion list for GROMACS users Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] adding SR2++ to charm27 force field Hi, Inspect the whole output. Is pdb2gmx picking up the version of charmm27 you think it is? Mark On Tue, Apr 14, 2015 at 8:40 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, I am trying to add SR 2++ in charm27 force field. I modified the ffnonbonded.itp, ffnanonbonded.itp, ions.itp, aminoacids,rtp, atomtypes.atp according to the parameters of SR in oplsaa.ff. However, when using pdb2gmx, I came across the following fatal error: Atomtype SR not found. Could anybody give me some advice? Thanks in advance, Ming -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to get the .gro file for MgO surface
You probably mean the topology, which you will have to build yourself, likely at the forcefield level. Is there any particular reason for trying to simulate metal oxide with GMX? There are much better tools suited for this, e.g. LAMMPS with ReaxFF. Alex z Dear you, z Does anyone know how to get the .gro file for MgO z surface? The pdb2gmx and Prodrg could not do that. z Best regards z Hongping -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] adding SR2++ to charm27 force field
Dear Justin and mark, I modified the files like this: aminoacids.rtp [ MG ] [ atoms ] MG MG 2.000 [ SR ] [ atoms ] SR SR 2.000 ions.itp [ moleculetype ] ; molname nrexcl MG 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 MG 1 MG MG 1 2 [ moleculetype ] ; molname nrexcl SR 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 SR 1 SR SR 1 2 ffnonbonded.itp CP1 MG 1 0.274842254546 0.051243325419 CP1 SR 1 0.3102690.494658 whenever there is MG, I add SR. ffnanonbonded.itp CN7 MG 1 0.274842254546 0.051243325419 CN7 SR 1 0.3102690.494658 whenever there is MG, I add SR. atomtypes.atp MG 24.305000 ; Magnesium Ion SR 87.62000 ; Strontium Ion When I copy the modified force field to the working directory, the PDB file used to consider MG Cannot be minimised too, which works well with the original Charmm27 force field. It reminds that atomtype SR not found again. I use ready-made pdb file and topol file for minimization. thanks -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Wednesday, 15 April 2015 1:22 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] adding SR2++ to charm27 force field On 4/14/15 5:12 AM, Ming Tang wrote: Hi Mark, Thanks for your reply. I am sure as I changed the files in the charmm27.ff installed in my unbuntu system. Is there any other things I need to consider? The files you listed are the only ones that should need to be modified. Either you missed a step and think you did something you didn't, or your changes didn't actually take effect (modifying the top-level installation usually requires admin privileges, so if you tried to modify without sudo or root it won't take). Experiment with a local copy of the directory rather than potentially messing up something system-wide. The error points most likely to the .atp file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to get the .gro file for MgO surface
On 4/14/15 10:10 PM, zhp1006 wrote: Dear you, Does anyone know how to get the .gro file for MgO surface? The pdb2gmx and Prodrg could not do that. Both of those are tools primarily for building topologies. If you have coordinates in a different format and want to convert to .gro (which is not necessary), simply use editconf. If you need to build a topology, probably x2top is the best bet. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to get the .gro file for MgO surface
Dear you, Does anyone know how to get the .gro file for MgO surface? The pdb2gmx and Prodrg could not do that. Best regards Hongping -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem with dihedral restraints in gromacs 5.0.4
On 4/10/15 12:06 PM, Agnieszka Slowicka wrote: Hello, I have a problem with implementation of dihedral restraints in gromacs 5.0.4. I introduced restraints into a topology file after the section with protein topology as fallowing: ; dihedral restraints added manually: phi,psi, chi1 and chi2 ; reference values = cluster 1 of charmm/tip4p [ dihedral_restraints ] ; ai ajakal type phi dphi kfac ; phi C(n-1) - N - CA - C 57 929 1-82 0 1 ; psi N - CA - C - N(n+1) 792930 1 1210 1 ; chi1 N - CA - CB - CG 791114 1-1770 1 ; chi1 CA - CB - CG - CD1 91114 15 1-1060 1 The previous version of the topology file with label and power parameters doesn't work generating error. I introduced the restraints section into the .mdp: ;dihedral restraints dihre = yes dihre_fc= 100 ; kJ/(mol rad^2) dihre_tau = 0.0 nstdihreout = 250 Gromacs works with this implementation but the restraints are not take into account. I don't see information about input parameters for dihedral restraints in my log file, however something is calculated because I found there: Energies (kJ/mol) BondU-BProper Dih. Improper Dih. LJ-14 1.71840e+016.93870e+014.03491e+017.20053e+00 4.07828e+01 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Dih. Rest. 1.80019e+026.68397e+03 -4.46824e+041.08339e+02 3.82359e-01 PotentialKinetic En. Total Energy Conserved En. Temperature I am sure that my restraints don't work because standard deviation of restrained angles is the same order like without restraints. Given that the energy associated with the dihedral restraints is 0.38 kJ/mol, I'd say they're just doing very little to help you :) The dihedral restraint options are ignored (well, technically they're removed) in an input .mdp file, and it seems that kfac is not a scaling factor at present, it is the actual force constant. That seems to agree with the fact that you're seeing a very light restraint with little effect. Try setting kfac equal to the actual force constant you want. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Hi Justin, Thank you for your suggestions. I introduced kfac=100 in my topology file instead of 1 and I think, it's working! So great thank you!! The dihedral energy reported in .log file is smaller then in the simulation calculated with gromacs 4.5.6, but my standard deviation of dihedral angles look similar to the restrained in the previous version which worked with the old parameters and topology very well. Do you have any idea why the parameters in the .mdp file are not wrote by gromacs 5.0.4? It could be explained in the manual as well, as the form of topology files with dihedral restraints. Thank you again, Agnieszka ~~~ Agnieszka M. Slowicka Department of Fluid Dynamics, Institute of Fundamental Technological Research, Polish Academy of Sciences, ul. Pawinskiego 5B; 02-106 Warsaw, Poland -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fatal error: Atom type Zn2+ (residue ZN) not found in atomtype database
I guess , the force filed you are using doesn't have ZN atom defined in atomtypes , you can define it manually or use other forcefileds which has it defined already On Thu, Apr 9, 2015 at 9:23 PM, Anurag Dobhal anurag.dob...@nano-medicine.co.in wrote: Dear all I am running pdb2gmx to creat the topology file of my structure, But I did get the error Fatal error: Atom type Zn2+ (residue ZN) not found in atomtype database Although my .pdb file does not contain Atom type Zn2+ (residue ZN) *Anurag DobhalJuniour Research fellowSupervisor: Dr. Ratnesh D. JainDepartment of chemical engineeringInsttute of Chemical Technology400019, +91 8898486877* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] A simple question
Can you please let me know what the problem is ? From: saeed poorasad s_poora...@yahoo.com To: Smith, Micholas D. smit...@ornl.gov; gmx-us...@gromacs.org gmx-us...@gromacs.org Sent: Tuesday, 14 April 2015, 9:59 Subject: Re: [gmx-users] A simple question Dear Dr.Smith , Thanks for your replay . This is a part of my PDB file : ATOM 1 CD1 TRP 1 19.910 19.430 16.500 1.00 0.00ATOM 2 CD1 TRP 1 20.210 20.850 16.560 1.00 0.00ATOM 3 CD1 TRP 1 19.010 21.540 16.970 1.00 0.00ATOM 4 CD1 TRP 1 17.960 20.560 17.150 1.00 0.00ATOM 5 CD1 TRP 1 18.520 19.250 16.860 1.00 0.00ATOM 6 CD1 TRP 1 19.090 22.640 17.820 1.00 0.00...I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field. Best regards ,Saeed. From: Smith, Micholas D. smit...@ornl.gov To: gmx-us...@gromacs.org gmx-us...@gromacs.org; saeed poorasad s_poora...@yahoo.com Sent: Monday, 13 April 2015, 21:24 Subject: Re: [gmx-users] A simple question Hi Saeed, Attachments don't work with the mailing list. Could you copy a few lines of the pdb for us to look at and maybe upload the pdb you generated to dropbox or a similar site? Also pdb2gmx may not be the best route here. You may need to explicitly write your own topology file (tedious as it may be), but lets take a closer look at what your pdb first. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of saeed poorasad s_poora...@yahoo.com Sent: Monday, April 13, 2015 2:29 AM To: gmx-us...@gromacs.org Subject: [gmx-users] A simple question Hi . Dear Gromacs users . Today is the first day that i am working with GROMACS .I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field. Can you please let me know what the problem is ? I have attached my PDB file with this Email. Best ,Saeed. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] there wasn't md_0_1.xtc file
Hi every body I have two questions? 1- accroding to the previos email, I used gromacs to run a covalent bond, for the first try,I run my covalent bond based on the tutorail (lysozyme in water) that nstxtcout = 0 was in md.mdp file, so I changed nstxtcout =0 to 0 and run was repeated. in the both try, I didn't achieve md_0_1.xtc. *I would like to know which parameters I should change to obtain this file?* 2- after finishing 1ns, I have several pdb files such as step0c.pdb, step1c.pdb, step1b.pdb, step2b.pdb, step2c.pdb. *please let me know I can use thses pdb files as a result?* thanks a lot best wishes *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and Biophysics (IBB)University of Tehran, Tehran- Iran.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fe2+ non bonded parameters for AMBER
Dear Users, Had anybody used Fe2+ ions in the active site of protein. I am planning to use one using amber99sb forcefield...please suggest to use the nonbonded parameters for Fe2+ ions, sigma and epsilon values. Kind regards, Raja -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Clusters
On Tue, Apr 14, 2015 at 2:45 AM, Lucas Dadalt Morero ld...@hotmail.com wrote: Sorry, it's 8 cores. Network is good. Good for what? I was hoping to hear that it's e.g IB QDR. Otherwise it's unlikely that you'll scale to all nodes. The hardware setup is ok, I just want to know how to perform a gromacs simulation using all the nodes.. Compile with MPI and run just like you'd run any MPI application. See if it scales at all on your network, if it does you can try tweaking the performance (e.g. PP-PME ratio, mutiple OpenMP threads per rank, nstlist, etc.) I suggest you check out that following page: http://www.gromacs.org/Documentation/Acceleration_and_parallelization -- Szilárd Lucas Date: Tue, 14 Apr 2015 02:06:49 +0200 From: pall.szil...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Clusters What network do you have? Unless it's fast (that is low latency) you won't be able to run across nodes. Are you sure about 9 cores, that number seems strange? -- Szilárd On Mon, Apr 13, 2015 at 11:52 PM, Lucas Dadalt Morero ld...@hotmail.com wrote: Are there any tutorial or tips to use cluster in Gromacs? I have 5 nodes with 9 cores each node and want use all them in one simulation, is that possible? I've read something about gromacs MPI but I don't know how to use. Can someone suggest some text or some tutorial for me? Thanks in advance, Lucas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to call an external LAPACK function in gromacs
Hi, Here is the information. Thank you. cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DCMAKE_PREFIX_PATH=/usr/lib64: Looking for sgemm_ -- Looking for sgemm_ - found -- A library with BLAS API found. -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Found the ability to use plug-ins when building shared libaries, so will compile to use plug-ins (e.g. to read VMD-supported file formats) . Configuring done make . Linking CXX executable ../../bin/template /usr/bin/c++-march=core-avx2 -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -rdynamic ../../lib/libgromacs.so.0.0.0 -fopenmp -ldl -lrt -lm -lfftw3f -lblas -llapack -lblas -llapack -lpthread -Wl,-rpath,/home/qw9/Downloads/gromacs-5.0/build/lib ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 Sincerely, Qian On Tue, Apr 14, 2015 at 3:56 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, When you ran cmake originally, what did it report about which LAPACK it found and will use? (You may need to clean your build tree and start again in order to find this out.) What is the linker command line now (e.g. make VERBOSE=1) Mark On Mon, Apr 13, 2015 at 11:30 PM, qian wang qq.wang...@gmail.com wrote: Dear All, I am a new user of gromacs 5.0. For my own purposes I made small changes in a gromacs source code where I called a function named DPOTRF. This is a standard function in LAPACK library but not in the gromacs internal LAPACK library. Now I have a problem of compiling. What I did is: cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DCMAKE_PREFIX_PATH=/usr/lib64 (this is the path of my extenal LAPACK library) this step is ok but next when I make, the error I got is: Linking CXX executable ../../bin/template ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 Could anyone help me with this problem? Thanks a lot. Sincerely, Qian -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to call an external LAPACK function in gromacs
Hi, I just found that changing from dpotrf to dpotrf_ in the source code would solve the problem... sorry for the trouble. Sincerely, Qian On Tue, Apr 14, 2015 at 3:11 PM, qian wang qq.wang...@gmail.com wrote: Hi, * Please try the latest 5.0.4 release, we might well have fixed a bug in the template compilation stuff.* I just tried 5.0.4 and have the same error. * Even then, per the README you will find in share/template, you will might have to teach CMake that it should augment the linking path.* Sorry I do not quite understand what it means. Could you please explain a bit more specific on what I should do next? Thanks for your time. Sincerely, Qian On Tue, Apr 14, 2015 at 12:34 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, On Tue, Apr 14, 2015 at 4:15 PM, qian wang qq.wang...@gmail.com wrote: Hi, Here is the information. Thank you. cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DCMAKE_PREFIX_PATH=/usr/lib64: Looking for sgemm_ -- Looking for sgemm_ - found -- A library with BLAS API found. -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Found the ability to use plug-ins when building shared libaries, so will compile to use plug-ins (e.g. to read VMD-supported file formats) . Configuring done OK, it did find your LAPACK. make . Linking CXX executable ../../bin/template /usr/bin/c++-march=core-avx2 -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -rdynamic ../../lib/libgromacs.so.0.0.0 -fopenmp -ldl -lrt -lm -lfftw3f -lblas -llapack -lblas -llapack -lpthread -Wl,-rpath,/home/qw9/Downloads/gromacs-5.0/build/lib ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 That works for me (i.e. the linker line has system BLAS and LAPACK libraries). Please try the latest 5.0.4 release, we might well have fixed a bug in the template compilation stuff. In any case, in 5.0.x the intended use case for the template is to install GROMACS, and then copy the installed template machinery somewhere so you can use it. Even then, per the README you will find in share/template, you will might have to teach CMake that it should augment the linking path. Mark Sincerely, Qian On Tue, Apr 14, 2015 at 3:56 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, When you ran cmake originally, what did it report about which LAPACK it found and will use? (You may need to clean your build tree and start again in order to find this out.) What is the linker command line now (e.g. make VERBOSE=1) Mark On Mon, Apr 13, 2015 at 11:30 PM, qian wang qq.wang...@gmail.com wrote: Dear All, I am a new user of gromacs 5.0. For my own purposes I made small changes in a gromacs source code where I called a function named DPOTRF. This is a standard function in LAPACK library but not in the gromacs internal LAPACK library. Now I have a problem of compiling. What I did is: cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DCMAKE_PREFIX_PATH=/usr/lib64 (this is the path of my extenal LAPACK library) this step is ok but next when I make, the error I got is: Linking CXX executable ../../bin/template ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 Could anyone help me with this problem? Thanks a lot. Sincerely, Qian -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list
Re: [gmx-users] Position restraint for ions
*Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? And surprisingly, if I remove the water with 'editconf', and only then I merge them using pdb2gmx, then the topology is written right (with the ions and zero net charge). Confusing, han? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Position restraint for ions
2015-04-14 14:54 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 4/14/15 1:48 PM, Marcelo Depólo wrote: Hi! I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group non-Water'* - to create an index for my RNA and Ions; and: *genrestr -f rna_ions.gro -n rna_ion.ndx -o rna_ion.itp -fc 800 800 800* - to create an .itp file for them. I am also including this new .itp file to the topology using the proper 'ifdef' statements, but I get this when I run grompp: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Position restraint for ions
On 4/14/15 3:25 PM, Marcelo Depólo wrote: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? And surprisingly, if I remove the water with 'editconf', and only then I merge them using pdb2gmx, then the topology is written right (with the ions and zero net charge). Confusing, han? I can offer no rationalization without seeing your commands and perhaps getting access to your files. Merging RNA+ions is something I do routinely, but I always do that before adding any water or anything else. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to call an external LAPACK function in gromacs
Hi, * Please try the latest 5.0.4 release, we might well have fixed a bug in the template compilation stuff.* I just tried 5.0.4 and have the same error. * Even then, per the README you will find in share/template, you will might have to teach CMake that it should augment the linking path.* Sorry I do not quite understand what it means. Could you please explain a bit more specific on what I should do next? Thanks for your time. Sincerely, Qian On Tue, Apr 14, 2015 at 12:34 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, On Tue, Apr 14, 2015 at 4:15 PM, qian wang qq.wang...@gmail.com wrote: Hi, Here is the information. Thank you. cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DCMAKE_PREFIX_PATH=/usr/lib64: Looking for sgemm_ -- Looking for sgemm_ - found -- A library with BLAS API found. -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Found the ability to use plug-ins when building shared libaries, so will compile to use plug-ins (e.g. to read VMD-supported file formats) . Configuring done OK, it did find your LAPACK. make . Linking CXX executable ../../bin/template /usr/bin/c++-march=core-avx2 -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -rdynamic ../../lib/libgromacs.so.0.0.0 -fopenmp -ldl -lrt -lm -lfftw3f -lblas -llapack -lblas -llapack -lpthread -Wl,-rpath,/home/qw9/Downloads/gromacs-5.0/build/lib ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 That works for me (i.e. the linker line has system BLAS and LAPACK libraries). Please try the latest 5.0.4 release, we might well have fixed a bug in the template compilation stuff. In any case, in 5.0.x the intended use case for the template is to install GROMACS, and then copy the installed template machinery somewhere so you can use it. Even then, per the README you will find in share/template, you will might have to teach CMake that it should augment the linking path. Mark Sincerely, Qian On Tue, Apr 14, 2015 at 3:56 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, When you ran cmake originally, what did it report about which LAPACK it found and will use? (You may need to clean your build tree and start again in order to find this out.) What is the linker command line now (e.g. make VERBOSE=1) Mark On Mon, Apr 13, 2015 at 11:30 PM, qian wang qq.wang...@gmail.com wrote: Dear All, I am a new user of gromacs 5.0. For my own purposes I made small changes in a gromacs source code where I called a function named DPOTRF. This is a standard function in LAPACK library but not in the gromacs internal LAPACK library. Now I have a problem of compiling. What I did is: cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DCMAKE_PREFIX_PATH=/usr/lib64 (this is the path of my extenal LAPACK library) this step is ok but next when I make, the error I got is: Linking CXX executable ../../bin/template ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 Could anyone help me with this problem? Thanks a lot. Sincerely, Qian -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
[gmx-users] R-B dihedrals
I have a set of dihedrals described by the R-B potential, with a minimum at 90 degrees, and minimization indeed yielded angles very close to that. At some point, I decided to check if I can rotate the groups to another angle, say, 45 degrees. Simple enough, so I changed the expression. Energy minimization shows no difference -- still 90 deg. I turned off vdw for all atoms in the vicinity, set all charges to zero -- no difference. Hiked up the dihedral constant by three(!) orders of magnitude -- nothing. Commenting out these dihedrals immediately causes grompp errors, so they are definitely seen by the system (I tracked the errors to the atomtypes). The dihedral type (3) is listed correctly in the topology. A David Lynch mystery. Any ideas? Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] R-B dihedrals
Hi Alex, Maybe writing out the preprocessed topology (grompp -pp) or checking the .tpr with gmxdump can show whether the dihedral parameters are really what you think they are. Cheers, Tsjerk On Apr 14, 2015 10:32 PM, Alex nedoma...@gmail.com wrote: I have a set of dihedrals described by the R-B potential, with a minimum at 90 degrees, and minimization indeed yielded angles very close to that. At some point, I decided to check if I can rotate the groups to another angle, say, 45 degrees. Simple enough, so I changed the expression. Energy minimization shows no difference -- still 90 deg. I turned off vdw for all atoms in the vicinity, set all charges to zero -- no difference. Hiked up the dihedral constant by three(!) orders of magnitude -- nothing. Commenting out these dihedrals immediately causes grompp errors, so they are definitely seen by the system (I tracked the errors to the atomtypes). The dihedral type (3) is listed correctly in the topology. A David Lynch mystery. Any ideas? Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Position restraint for ions
2015-04-14 17:26 GMT-03:00 Justin Lemkul jalem...@vt.edu On 4/14/15 3:25 PM, Marcelo Depólo wrote: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? And surprisingly, if I remove the water with 'editconf', and only then I merge them using pdb2gmx, then the topology is written right (with the ions and zero net charge). Confusing, han? I can offer no rationalization without seeing your commands and perhaps getting access to your files. Merging RNA+ions is something I do routinely, but I always do that before adding any water or anything else. So how do you insert your ions without water to be exchanged for the ions? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil) B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Position restraint for ions
On 4/14/15 4:50 PM, Marcelo Depólo wrote: 2015-04-14 17:26 GMT-03:00 Justin Lemkul jalem...@vt.edu On 4/14/15 3:25 PM, Marcelo Depólo wrote: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section position_restraintsin a part belonging to a different molecule than you intended to.In that case move the position_restraints section to the right molecule.* It seems the ions are not included as the same moleculetype as the RNA and Gromacs see this as an error. Would someone knows a neat way to do this? The ions need to be merged into the RNA [moleculetype] definition in order for this to work. This isn't something that is done after the fact with index groups as you're trying above; the topologies need to be merged, e.g. with pdb2gmx -chainsep -merge, or by hand if the ions aren't part of the input coordinate file. Thanks, Justin. I have tried that by using '-merge all' but this created a .top without the ions. RNA and water only. grompp even warned me that my system now has non-zero charge. Any ideas? And surprisingly, if I remove the water with 'editconf', and only then I merge them using pdb2gmx, then the topology is written right (with the ions and zero net charge). Confusing, han? I can offer no rationalization without seeing your commands and perhaps getting access to your files. Merging RNA+ions is something I do routinely, but I always do that before adding any water or anything else. So how do you insert your ions without water to be exchanged for the ions? I don't restraint bulk ions. I'm only interested in structurally bound ions, and there are various reasons to restrain those during different processes. Why do you want to restrain bulk ions? You should be able to do whatever you like, but without more information I can't diagnose what's happening in your case. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] R-B dihedrals
On 4/14/15 5:12 PM, Alex wrote: Tried both, the (now enormous) parameters are read in correctly, nothing in output mdp that catches my eye. No constraints used in the system, explicitly set in mdp. Plotted the potential at 45/315 deg minimum -- definitely nonzero at 90 degrees (starting config). This has got to be the strangest GMX issue i've ever had. What does a 1-D energy surface look like for that dihedral? You've got a dihedral at 90 in the coordinates and you're trying to shift it to 45? If there's a massive barrier in between, EM won't necessarily do that for you. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] R-B dihedrals
Absolutely nothing in between, this is (cos(45)-cos(phi))^2, two minima at 45 and 315 and a peak around 180. Checked if I converted to R-B coefficients correctly -- same thing. At 90/270 clean decrease to 45/315. Alex On Tue, Apr 14, 2015 at 3:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/14/15 5:12 PM, Alex wrote: Tried both, the (now enormous) parameters are read in correctly, nothing in output mdp that catches my eye. No constraints used in the system, explicitly set in mdp. Plotted the potential at 45/315 deg minimum -- definitely nonzero at 90 degrees (starting config). This has got to be the strangest GMX issue i've ever had. What does a 1-D energy surface look like for that dihedral? You've got a dihedral at 90 in the coordinates and you're trying to shift it to 45? If there's a massive barrier in between, EM won't necessarily do that for you. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] R-B dihedrals
Can you shift it to 40 degrees? Mark On Tue, Apr 14, 2015 at 11:26 PM, Alex nedoma...@gmail.com wrote: Absolutely nothing in between, this is (cos(45)-cos(phi))^2, two minima at 45 and 315 and a peak around 180. Checked if I converted to R-B coefficients correctly -- same thing. At 90/270 clean decrease to 45/315. Alex On Tue, Apr 14, 2015 at 3:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/14/15 5:12 PM, Alex wrote: Tried both, the (now enormous) parameters are read in correctly, nothing in output mdp that catches my eye. No constraints used in the system, explicitly set in mdp. Plotted the potential at 45/315 deg minimum -- definitely nonzero at 90 degrees (starting config). This has got to be the strangest GMX issue i've ever had. What does a 1-D energy surface look like for that dihedral? You've got a dihedral at 90 in the coordinates and you're trying to shift it to 45? If there's a massive barrier in between, EM won't necessarily do that for you. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] R-B dihedrals
Mark, we just figured it out, thanks. :) And yes, you are definitely onto something: two identical dihedrals pulling in opposite directions. This is what happens when people from solid state show up to use GMX. :) Alex On Tue, Apr 14, 2015 at 5:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Can you shift it to 40 degrees? Mark On Tue, Apr 14, 2015 at 11:26 PM, Alex nedoma...@gmail.com wrote: Absolutely nothing in between, this is (cos(45)-cos(phi))^2, two minima at 45 and 315 and a peak around 180. Checked if I converted to R-B coefficients correctly -- same thing. At 90/270 clean decrease to 45/315. Alex On Tue, Apr 14, 2015 at 3:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/14/15 5:12 PM, Alex wrote: Tried both, the (now enormous) parameters are read in correctly, nothing in output mdp that catches my eye. No constraints used in the system, explicitly set in mdp. Plotted the potential at 45/315 deg minimum -- definitely nonzero at 90 degrees (starting config). This has got to be the strangest GMX issue i've ever had. What does a 1-D energy surface look like for that dihedral? You've got a dihedral at 90 in the coordinates and you're trying to shift it to 45? If there's a massive barrier in between, EM won't necessarily do that for you. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
