[gmx-users] a question on energygrps
Hello: I've got a question on energygrps options in .mdp file. This option is usually used for establishing the groups for the energy output. I am going to study the entropy changes of protein-ligand-SOL in a membrane system, I am just wondering shall I specify each compoenent in energygrps option, like: energygrps = Protein LIG SOL POPC I am also going to use g_lie for interaction analysis, will the above options be sufficient? If I forgot to assign the energygrps options in my md.mdp file during MD simulations, is it any fast way to calculate the energy after MD instead of running the simulation from beginning? I notice that there is a tool called g_lie can be used to evaluate protein/ligand binding, I am just wondering is there any paper on this tool? I don't find too much informations on gromacs manual. thank you very much Albert -- 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] Restraints influeincing free energy calculations
Hi all, Just a quick question - and perhaps some wisdom from those with more experience. I am trying to use metadynamics with gromacs to plot an energy landscape about the rotation of two proteins. If I were to define my collective variables as ThetaA and ThetaB, Theta being the rotation about the protein principle axis, I could sample identical rotations but at different distances apart. Therefore, this introduces the idea of a third collective variable, absolute distance between the centre-of-mass of the proteins. Given that I don't actually want to sample space where these two proteins are beyond peptide-peptide interactions, it is of little interest plus would be extremely computationally crippling, I thought I could apply a restraint between the two proteins at a distance previously identified in literature using FRET. My two questions: 1) Would applying a restraint mess with or bias free energy calculations in any form of free energy calculations, be it, metadynamics or umbrella sampling, and, 2) words of wisdom from anyone who has undertaken such a problem? Many thanks Anthony -- 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] a question on energygrps
On 7/14/13 6:21 AM, Albert wrote: Hello: I've got a question on energygrps options in .mdp file. This option is usually used for establishing the groups for the energy output. I am going to study the entropy changes of protein-ligand-SOL in a membrane system, I am just wondering shall I specify each compoenent in energygrps option, like: energygrps = Protein LIG SOL POPC This setting will give you pairwise-decomposed nonbonded energies between these groups, but it has nothing to do with entropy. I am also going to use g_lie for interaction analysis, will the above options be sufficient? No. The LIE method requires a separate simulation of the ligand in water to acquire ligand-water interaction energies. In the case of a heterogeneous system like yours (including a membrane), I don't know that the LIE assumptions hold since you don't necessarily have simple partitioning between aqueous and protein-bound states. If I forgot to assign the energygrps options in my md.mdp file during MD simulations, is it any fast way to calculate the energy after MD instead of running the simulation from beginning? That's what mdrun -rerun is for. I notice that there is a tool called g_lie can be used to evaluate protein/ligand binding, I am just wondering is there any paper on this tool? I don't find too much informations on gromacs manual. Nor should you - the manual is not a definitive repository of all MD-related knowledge :) The literature for LIE is extensive in terms of both primary literature and review articles. Apply Google or your favorite scientific database. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] qm-mm calculation
Hello, I am trying to run the qm-mm gas phase calculations for my system. I am using following in md.mdp file. title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001; ps ! nsteps = 500 ; total 5 ps. nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 1 nstlist = 1 ns_type = simple rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 coulombtype = cut-off vdwtype = cut-off pbc = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = nose-hoover tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = no ;Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 350.0 gen_seed= 173529 QMMM = yes QMMM-grps= System QMmethod = RHF QMbasis = 3-21G QMcharge = 0 QMmult = 1 I could run the grompp and for mdrun I am getting following error. Back Off! I just backed up md.log to ./#md.log.2# Reading file 1.tpr, VERSION 4.0.7 (single precision) QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 32 QMlevel: RHF/3-21G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 [c63:25888] *** Process received signal *** [c63:25888] Signal: Segmentation fault (11) [c63:25888] Signal code: Address not mapped (1) [c63:25888] Failing at address: (nil) [c63:25888] [ 0] /lib64/libpthread.so.0 [0x2b2d89ac1a90] [c63:25888] [ 1] /lib64/libc.so.6(strlen+0x40) [0x2b2d89d4b590] [c63:25888] [ 2] /lib64/libc.so.6(fputs+0x1e) [0x2b2d89d33dde] [c63:25888] [ 3] mdrun(init_gaussian+0x4c3) [0x51e993] [c63:25888] [ 4] mdrun(init_QMMMrec+0xef8) [0x517578] [c63:25888] [ 5] mdrun(mdrunner+0x1019) [0x42e109] [c63:25888] [ 6] mdrun(main+0x3c5) [0x434b95] [c63:25888] [ 7] /lib64/libc.so.6(__libc_start_main+0xe6) [0x2b2d89ced586] [c63:25888] [ 8] mdrun [0x415cb9] [c63:25888] *** End of error message *** Segmentation fault Could you tell what is the problem. 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
[gmx-users] How to compile Cygwin 4.6.3 for Windows using Cygwin
Hello, How to compile Cygwin 4.6.3 for Windows using Cygwin ? I did so: tar xfz gromacs-4.6.tar.gz cd gromacs-4.6 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON (fftw 3.3 - install) make Error message Thank you. -- 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] qm-mm calculation
On 7/14/13 11:36 AM, Nilesh Dhumal wrote: Hello, I am trying to run the qm-mm gas phase calculations for my system. I am using following in md.mdp file. title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001; ps ! nsteps = 500 ; total 5 ps. nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 1 nstlist = 1 ns_type = simple rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 coulombtype = cut-off vdwtype = cut-off pbc = no fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = nose-hoover tau_t = 0.1 tc-grps =system ref_t = 350 ; Pressure coupling is on Pcoupl = no ;Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 350.0 gen_seed= 173529 QMMM = yes QMMM-grps= System QMmethod = RHF QMbasis = 3-21G QMcharge = 0 QMmult = 1 I could run the grompp and for mdrun I am getting following error. Back Off! I just backed up md.log to ./#md.log.2# Reading file 1.tpr, VERSION 4.0.7 (single precision) QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 32 QMlevel: RHF/3-21G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 [c63:25888] *** Process received signal *** [c63:25888] Signal: Segmentation fault (11) [c63:25888] Signal code: Address not mapped (1) [c63:25888] Failing at address: (nil) [c63:25888] [ 0] /lib64/libpthread.so.0 [0x2b2d89ac1a90] [c63:25888] [ 1] /lib64/libc.so.6(strlen+0x40) [0x2b2d89d4b590] [c63:25888] [ 2] /lib64/libc.so.6(fputs+0x1e) [0x2b2d89d33dde] [c63:25888] [ 3] mdrun(init_gaussian+0x4c3) [0x51e993] [c63:25888] [ 4] mdrun(init_QMMMrec+0xef8) [0x517578] [c63:25888] [ 5] mdrun(mdrunner+0x1019) [0x42e109] [c63:25888] [ 6] mdrun(main+0x3c5) [0x434b95] [c63:25888] [ 7] /lib64/libc.so.6(__libc_start_main+0xe6) [0x2b2d89ced586] [c63:25888] [ 8] mdrun [0x415cb9] [c63:25888] *** End of error message *** Segmentation fault Could you tell what is the problem. Debugging code that is nearly 4 years old is not very productive for the development team. If you can reproduce the problem with version 4.6.3, it's more likely to get attention, as countless changes, enhancements, and improvements have taken place in the intervening time, any of which may have implications for whatever it is that you're trying to do. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] How to compile Cygwin 4.6.3 for Windows using Cygwin
On 7/14/13 1:04 PM, bh...@udsu.ru wrote: Hello, How to compile Cygwin 4.6.3 for Windows using Cygwin ? I did so: tar xfz gromacs-4.6.tar.gz cd gromacs-4.6 The version 4.6 tarball will not give you version 4.6.3 :) Unless this is a typo, make sure you're actually working with the newest version. mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON (fftw 3.3 - install) make Error message Please copy and paste the actual error message. Simply saying there's an error leaves it impossible to help you. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] How to compile Cygwin 4.6.3 for Windows using Cygwin
Error message, аfter the make: In file included from /cygdrive/d/1/gromacs-4.6.3/src/gmxlib/thread_mpi/atomic.c:38:0: /cygdrive/d/1/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20: ошибка: field «timer_init» has incomplete type src/gmxlib/CMakeFiles/gmx.dir/build.make:8061: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o' failed make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o] Error 1 CMakeFiles/Makefile2:1238: recipe for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 On 7/14/13 1:04 PM, bh...@udsu.ru wrote: Hello, How to compile Cygwin 4.6.3 for Windows using Cygwin ? I did so: tar xfz gromacs-4.6.tar.gz cd gromacs-4.6 The version 4.6 tarball will not give you version 4.6.3 :) Unless this is a typo, make sure you're actually working with the newest version. mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON (fftw 3.3 - install) make Error message Please copy and paste the actual error message. Simply saying there's an error leaves it impossible to help you. -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] acidic pH
Hello dear users I'm simulating gold nanoparticle interaction with protein. I want to change the pH of system. What would need to be changed to simulate this system at pH 3.0? thanks you Fatemeh Ramezani -- 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] acidic pH
On 7/14/13 2:23 PM, fatemeh ramezani wrote: Hello dear users I'm simulating gold nanoparticle interaction with protein. I want to change the pH of system. What would need to be changed to simulate this system at pH 3.0? As is discussed frequently on this list (hint: check the archive for some very good discussions), the concept of pH in an MD simulation system is relatively ill-defined in a classical simulation. Protonation states are fixed in normal MD, so the only thing you can really do is approximate the effect of pH by protonating the amino acids in their most prevalent form at that pH. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Cyclic Peptide Topology
Hi, I'm want to run a MD simulation with a Phe-Phe-Phe-Phe-Gly cyclic peptide. But I'm have problems generating the topology files. When I try to use the strategy to generate a topology file for the linear GF using pdb2gmx -ff charmm27 -f pep.pdb -o pep.gro -ter -water spce and choosing None for both termini I will get the following error --- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/johnny/gromacs-4.6.3/src/kernel/pdb2top.c, line: 110 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coorate file, add a new terminal database entry (.tdb), or select the proper exing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Has anybody an idea how i can overcome this problem or some kind of tutorial to generate the topologies files for a cyclic peptide ? Thanks in advance Cheers Jan -- View this message in context: http://gromacs.5086.x6.nabble.com/Cyclic-Peptide-Topology-tp5009832.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Cyclic Peptide Topology
On 7/14/13 7:07 PM, jriedel wrote: Hi, I'm want to run a MD simulation with a Phe-Phe-Phe-Phe-Gly cyclic peptide. But I'm have problems generating the topology files. When I try to use the strategy to generate a topology file for the linear GF using pdb2gmx -ff charmm27 -f pep.pdb -o pep.gro -ter -water spce and choosing None for both termini I will get the following error --- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/johnny/gromacs-4.6.3/src/kernel/pdb2top.c, line: 110 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coorate file, add a new terminal database entry (.tdb), or select the proper exing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Has anybody an idea how i can overcome this problem or some kind of tutorial to generate the topologies files for a cyclic peptide ? pdb2gmx is not designed to produce topologies for cyclic peptides. Check the archive for numerous threads on this topic. Perhaps a specbond.dat entry will help, otherwise the sure-fire solution is to manually add the required bonded terms (bond, angles, and dihedrals) to the topology after pdb2gmx does its work. The above error can likely be overcome by using -missing (which is OK in this instance, but not in many other cases). -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Figures of PCA analysis
Can anybody help me understand these better? 2013/7/10 lloyd riggs lloyd.ri...@gmx.ch There vectors. Theres some good older papers explaining the whole thing from Van Gunstern, Berendsen, and some other good ones from de Groot that explain them well and includes combining them with other data analysis types, but I dont remeber the actual publications. A few are in the mid 1990's, however these explain PCA better than some of the newer ones...but some extensive reading...or text books from van guntstern and/or Berendsen explain the whole thing well, from the math to the actual what it means aspect. *Gesendet:* Mittwoch, 10. Juli 2013 um 14:46 Uhr *Von:* Ahmet yıldırım ahmedo...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Figures of PCA analysis Dear users, I have a few questions about PCA analysis. I see the figures below in the most of the publications: 1.) Figure:Eigenvalues along the eigenvectors This figure gives contribution of eigenvalues along the eigenvectors to the overall motion of the protein??? 2.) Figure:the projection of the MD trajectories onto the first ten principal components This figure gives contribution of the first 10 eigenvectors to the overall motion of the protein??? 3.)The projection of the MD trajectories onto the plane of the first and the second principal components This figure gives knowledge about conformational spaces of structures??? Which one gives information about the motion of the structure? Can anyone explain to me in detail what these figure are? -- Ahmet Yıldırım -- 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 -- Ahmet Yıldırım -- 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: extreme projections
any one please help me out with this problem? 2013/7/10 Ahmet yıldırım ahmedo...@gmail.com Dear users, I extracted separate extreme projections using g_anaeig. I have to make pictures which show the difference. Can you help me, someone who makesthem using pymolbefore ? -- Ahmet Yıldırım -- Ahmet Yıldırım -- 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] snapshot
Hi, How to get a snapshots in equal intervals of time (250ps) from production MD trajectory. I'm using -sep , -t0, -timestep but output came only one .gro file. -- View this message in context: http://gromacs.5086.x6.nabble.com/snapshot-tp5009837.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] snapshot
On 7/14/13 9:03 PM, Rama wrote: Hi, How to get a snapshots in equal intervals of time (250ps) from production MD trajectory. I'm using -sep , -t0, -timestep but output came only one .gro file. trjconv -skip -sep should work, but without exact command lines and the output you received (as well as the output of gmxcheck on the trajectory), it's hard to be more specific. The -t0 and -timestep options will have no effect except to modify the trajectory - read the information in -h carefully! -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Figures of PCA analysis
Which papers have you read so far? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Ahmet yildirim Sent: Monday, 15 July 2013 9:41 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Figures of PCA analysis Can anybody help me understand these better? 2013/7/10 lloyd riggs lloyd.ri...@gmx.ch There vectors. Theres some good older papers explaining the whole thing from Van Gunstern, Berendsen, and some other good ones from de Groot that explain them well and includes combining them with other data analysis types, but I dont remeber the actual publications. A few are in the mid 1990's, however these explain PCA better than some of the newer ones...but some extensive reading...or text books from van guntstern and/or Berendsen explain the whole thing well, from the math to the actual what it means aspect. *Gesendet:* Mittwoch, 10. Juli 2013 um 14:46 Uhr *Von:* Ahmet yıldırım ahmedo...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Figures of PCA analysis Dear users, I have a few questions about PCA analysis. I see the figures below in the most of the publications: 1.) Figure:Eigenvalues along the eigenvectors This figure gives contribution of eigenvalues along the eigenvectors to the overall motion of the protein??? 2.) Figure:the projection of the MD trajectories onto the first ten principal components This figure gives contribution of the first 10 eigenvectors to the overall motion of the protein??? 3.)The projection of the MD trajectories onto the plane of the first and the second principal components This figure gives knowledge about conformational spaces of structures??? Which one gives information about the motion of the structure? Can anyone explain to me in detail what these figure are? -- Ahmet Yıldırım -- 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 -- Ahmet Yıldırım -- 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
