Re: [gmx-users] Version problem
On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote: Dear all, I am new to GROMACS, just finish installation of v5.0.2, started reading online manual, as instructed executed the command: mdrun -version and the printout pasted below. It is printing GROMACS version 4.6.5, however I have installed version 5.0.2. What is the problem? Find the directory to where you have installed your GROMACS 5.0 executables and then do source /path/to/gmx5/bin/GMXRC which mdrun should now give you the 5.0 mdrun Carsten Regards, Satyabrata Das == Program: mdrun Gromacs version:VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Sun Dec 15 04:01:11 UTC 2013 Built by: buildd@panlong [CMAKE] Build OS/arch: Linux 3.2.0-37-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5620 @ 2.40GHz Build CPU family: 6 Model: 44 Stepping: 2 Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2 C compiler flags: -msse4.1-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG satyabrata@satyabrata-desktop:~$ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Version problem
Dear Dr. Carsten Kutzner, I am unable to find the gmx5/bin/GMXRC in my machine, used 'locate' and 'find' to search the location. However I have source the following: source /usr/share/gromacs/shell-specific/GMXRC.bashrc Without this also mdrun is running. I am definitely missing something. Kindly help. With best regards, Satya On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote: Dear all, I am new to GROMACS, just finish installation of v5.0.2, started reading online manual, as instructed executed the command: mdrun -version and the printout pasted below. It is printing GROMACS version 4.6.5, however I have installed version 5.0.2. What is the problem? Find the directory to where you have installed your GROMACS 5.0 executables and then do source /path/to/gmx5/bin/GMXRC which mdrun should now give you the 5.0 mdrun Carsten Regards, Satyabrata Das == Program: mdrun Gromacs version:VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Sun Dec 15 04:01:11 UTC 2013 Built by: buildd@panlong [CMAKE] Build OS/arch: Linux 3.2.0-37-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5620 @ 2.40GHz Build CPU family: 6 Model: 44 Stepping: 2 Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2 C compiler flags: -msse4.1-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG satyabrata@satyabrata-desktop:~$ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] Version problem
Dear Satya, GMXRC is present in the installation directory. You need to find where you have installed the gromacs 5.0.2. Then locate the bin directory. GMXRC is generally present there. Chandan On Thu, Nov 6, 2014 at 2:00 PM, sa...@physics.iisc.ernet.in wrote: Dear Dr. Carsten Kutzner, I am unable to find the gmx5/bin/GMXRC in my machine, used 'locate' and 'find' to search the location. However I have source the following: source /usr/share/gromacs/shell-specific/GMXRC.bashrc Without this also mdrun is running. I am definitely missing something. Kindly help. With best regards, Satya On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote: Dear all, I am new to GROMACS, just finish installation of v5.0.2, started reading online manual, as instructed executed the command: mdrun -version and the printout pasted below. It is printing GROMACS version 4.6.5, however I have installed version 5.0.2. What is the problem? Find the directory to where you have installed your GROMACS 5.0 executables and then do source /path/to/gmx5/bin/GMXRC which mdrun should now give you the 5.0 mdrun Carsten Regards, Satyabrata Das == Program: mdrun Gromacs version:VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Sun Dec 15 04:01:11 UTC 2013 Built by: buildd@panlong [CMAKE] Build OS/arch: Linux 3.2.0-37-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5620 @ 2.40GHz Build CPU family: 6 Model: 44 Stepping: 2 Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2 C compiler flags: -msse4.1-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG satyabrata@satyabrata-desktop:~$ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India *All work and no play makes Jack a dull boy...”* -- 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] Pressure Question
Le 06/11/2014 06:16, Antonio Baptista a écrit : In particular, the virial-based instantaneous pressure (call it P') computed in simulations has its ensemble average equal to the thermodynamic pressure P (check any good book on molecular simulation). But, as others already pointed out, this P' is well-known to show extremelly large fluctuations, meaning that its average computed from the simulation has usually a very large statistical spread. In other words, although the ensemble average of P' is strictly equal to P, its simulation average is a random variable that often shows large deviations from P (especially for short simulations). To get an idea of what is an acceptable error for the average of P', you may look at its distribution histogram in the NPT simulation. Dear Antonio, Sorry if my message sound aggressive when I talked about totally irrevelevant, I will clarify my thoughts. From a theoretical point of view, you are right, each ensemble is accessible. From a biological point of view, though, the concept of fixing the volume is less reasonable: we live at constant pressure and temperature, and also at tighly controlled pH, and salt concentrations. The volume varies though, as you feel it when the weather is getting hot or cold. My point was exactly what your are telling in a more formal way than me: this P' is well-known to show extremely large fluctuations Well, digging a bit more on my feeling, I also found opposite arguments on the AMBER mailing list, like here: http://archive.ambermd.org/201103/0431.html So I'll got back again on my research and adjust my mind on the actual bleeding edge simulations taking into account all the recent code and force fields progresses. Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.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] Tested and most compatible Gromacs version for Mac OS Leopard (10.5)
Dear Gromacs Users, Please suggest me latest gromacs version which will suit Mac OS Leopard (on Apple cluster) without having any problems. Can it be possible to use 5.0 Gromacs series for the same?. I searched in net and mailing list didn't found any reliable answer. Thanking You in advance. Pavan Payghan -- 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] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500
Dear all, I observed that g_covar in Gromacs 5.0.2 segfaults at the diagonalization step, if the group for the covariance analysis is bigger than 500 atoms, i.e. if the covariance matrix is bigger than 1500x1500. In my hands, this problem does not arise with g_covar 4.6.x. The results obtained from g_covar (version 5.x) on groups = 500 atoms that I obtained were the same os those from version 4.6.x and also verified manually. Memory is not the problem here. The problem is independent on single/double precision. Before posting this on redmine.gromacs I first want to check whether someone here has made a contradicting experience which would argue against a possible bug introduced in 5.0.2? Thanks. Cheers, Jan-Philipp Machtens Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] centering a protofibril in a box
Dear all, I am trying to center a protofibril in a box, but respect to its first monomer. (the result would be the protofibril shiftted to the botton of the box) I used trjconv -f protofibril.pdb -n index.ndx -center -s protofibril.pdb -o test.pdb I did an index for the residues corresponding to the first monomer and that is which I chose as select group for centering but when I visualize the System with vmd the protofibril appears in the center of the box but as it was just one molecule. Thanks in advance! Adriana -- 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] md.log interpretation
I have tried running simulation with zero cutoff and zero nstlist and simple ns. That was very very slow, however. anyway thanks for the reply. On Nov 5, 2014 9:38 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I am not familiar with the implementation details, but I would assume there is a dependency on rcoulomb of the cost of the Born force chain rule. You can check this by trying different values. It might be faster to use infinite cutoffs (see manual) so that the algorithm does not need to search. Mark On Tue, Nov 4, 2014 at 1:34 AM, Nizar Masbukhin nizar.fku...@gmail.com wrote: Dear gromacs users, I've just finished my NVT equilibration in implicit solvent. From md.log, i see that most of time were used to calculate Forces (of Born force chain rule). Could someone explain to me why calculating it takes so long? mdp setting: integrator=md dt=0.004 nstep=250 bd-frict=50 rlist=5 rvdw=5 rcoulomb=5 nstlist=40 implicit-solvent=GBSA gb-alogarithm=still nstgbradii=40 gbradii=5 gb-epsilon-solvent=80 gb-salt-conc=0.2 sa-algorithm=ace-approximation sa-surface-tension=2.05 constraints=all-bonds constraints-algorithm=LINCS lincs-order=12 md.log M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - NB VdW [VF] 32677.013279 32677.013 0.0 NB VdW [F] 1740991.575264 1740991.575 0.3 NB VdW Elec. [VF] 1192677.312698 1192677.313 0.2 NB VdW Elec. [F] 106409048.599622 106409048.600 17.9 1,4 nonbonded interactions 20035.628466 1803206.562 0.3 Born radii (Still) 1999216.23274293963162.939 15.8 Born force chain rule 25548182.811729 *383222742.176* 64.4 NS-Pairs 64906.572700 1363038.027 0.2 CG-CoM 205.506576 616.520 0.0 Propers 15168.313980 3473543.901 0.6 Impropers 637.980588 132699.962 0.0 Pos. Restr. 3830.053530 191502.676 0.0 Virial 82.6954711488.518 0.0 Stop-CM 82.214752 822.148 0.0 Calc-Ekin 822.011152 22194.301 0.0 Lincs 4696.969329 281818.160 0.0 Lincs-Mat 229529.791548 918119.166 0.2 Constraint-V 9393.938658 75151.509 0.0 Constraint-Vir 46.9739791127.375 0.0 Virtual Site 3 615.868824 22787.146 0.0 Virtual Site 3fd 791.205144 75164.489 0.0 Virtual Site 3fad 168.761208 29701.973 0.0 Virtual Site 3out 1893.632256 164746.006 0.0 Virtual Site 4fdn 576.418152 146410.211 0.0 (null) 476.315439 0.000 0.0 - Total 595265438.267 100.0 - R E A L C Y C L E A N D T I M E A C C O U N T I N G On 1 MPI rank Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Vsite constr. 111085001 96.421385.432 0.2 Neighbor search11 27126 915.964 3661.462 2.1 Force 111085001 *39317.742* 157168.118 91.3 Vsite spread 111095852 142.563569.880 0.3 Write traj.11 11030 425.764 1701.942 1.0 Update 111085001 96.742386.714 0.2 Constraints1110850011311.720 5243.449 3.0 Rest 766.404 3063.612 1.8 - Total 43073.320 172180.608 100.0
Re: [gmx-users] Version problem
tried which mdrun showing the path /usr/bin/mdrun, which v4.6.5, however I have downloaded v5.0.2.tar.gz and used for installation. try to find mdrun program by typing this command on terminal: which mdrun will show path of mdrun program where it located. On Nov 6, 2014 4:01 PM, sa...@physics.iisc.ernet.in wrote: Dear Dr. Carsten Kutzner, I am unable to find the gmx5/bin/GMXRC in my machine, used 'locate' and 'find' to search the location. However I have source the following: source /usr/share/gromacs/shell-specific/GMXRC.bashrc Without this also mdrun is running. I am definitely missing something. Kindly help. With best regards, Satya On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote: Dear all, I am new to GROMACS, just finish installation of v5.0.2, started reading online manual, as instructed executed the command: mdrun -version and the printout pasted below. It is printing GROMACS version 4.6.5, however I have installed version 5.0.2. What is the problem? Find the directory to where you have installed your GROMACS 5.0 executables and then do source /path/to/gmx5/bin/GMXRC which mdrun should now give you the 5.0 mdrun Carsten Regards, Satyabrata Das == Program: mdrun Gromacs version:VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Sun Dec 15 04:01:11 UTC 2013 Built by: buildd@panlong [CMAKE] Build OS/arch: Linux 3.2.0-37-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5620 @ 2.40GHz Build CPU family: 6 Model: 44 Stepping: 2 Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2 C compiler flags: -msse4.1-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG satyabrata@satyabrata-desktop:~$ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and
[gmx-users] Minimization is not running
Dear all, I am just new to GROMACS, tried to install v5.0.2, although isntallation was successful, while running it is giving problem: I am just trying to do the lysozyme tutorial, however first energy minimization is not running, mdrun stopped with: === Reading file em.tpr, VERSION 4.6.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads Compiled acceleration: SSE4.1 (Gromacs could use SSE2 on this machine, which is better) Back Off! I just backed up em.trr to ./#em.trr.1# Back Off! I just backed up em.edr to ./#em.edr.1# Illegal instruction (core dumped) I have attached log file which shows during installation compiler flag SSE4.1 was used instead of SSE2, how to fix this? With best regards, Satyabrata Das -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] Minimization is not running
This is because you are using 4.6.5 provided by your OS, and it has been compiled assuming SSE4.1, but your machine is so old it only runs SSE2. When you find your 5.0.2 install, it will be probably compiled for SSE2. Mark On Thu, Nov 6, 2014 at 12:52 PM, sa...@physics.iisc.ernet.in wrote: Dear all, I am just new to GROMACS, tried to install v5.0.2, although isntallation was successful, while running it is giving problem: I am just trying to do the lysozyme tutorial, however first energy minimization is not running, mdrun stopped with: === Reading file em.tpr, VERSION 4.6.5 (single precision) Using 1 MPI thread Using 2 OpenMP threads Compiled acceleration: SSE4.1 (Gromacs could use SSE2 on this machine, which is better) Back Off! I just backed up em.trr to ./#em.trr.1# Back Off! I just backed up em.edr to ./#em.edr.1# Illegal instruction (core dumped) I have attached log file which shows during installation compiler flag SSE4.1 was used instead of SSE2, how to fix this? With best regards, Satyabrata Das -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500
Hi, yes I will post that to redmine soon, but let me first clarify the issue, since I tested some more conditions in the meantime. (I realized that my trajectory had 1501 frames and the error occured when I choose more than 500 atoms, i.e. when the number of degrees of freedom becomes larger then the number of frames). So in general, if your trajectory has nf frames, g_covar will result in a segfault if the group to be (covariance) analyzed is larger then nf/3 atoms. If found this statement to be true for gromacs 4.6.6, 4.6.7 and 5.0.2. This error does not happen for gromacs 4.6.5 So, I wonder whether this is an unwanted behaviour which has been introduced in 4.6.6? Do you think this behavior makes sense ? The official release notes for 4.6.6 do not mention changes in g_covar. Best, Jan-Philipp Machtens From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: Thursday, November 06, 2014 1:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500 Hi, IIRC some minor bugs were fixed, but a regression like that should be dealt with... please file at http://redmine.gromacs.org. Mark On Thu, Nov 6, 2014 at 12:00 PM, Machtens, Jan-Philipp j.macht...@fz-juelich.de wrote: Dear all, I observed that g_covar in Gromacs 5.0.2 segfaults at the diagonalization step, if the group for the covariance analysis is bigger than 500 atoms, i.e. if the covariance matrix is bigger than 1500x1500. In my hands, this problem does not arise with g_covar 4.6.x. The results obtained from g_covar (version 5.x) on groups = 500 atoms that I obtained were the same os those from version 4.6.x and also verified manually. Memory is not the problem here. The problem is independent on single/double precision. Before posting this on redmine.gromacs I first want to check whether someone here has made a contradicting experience which would argue against a possible bug introduced in 5.0.2? Thanks. Cheers, Jan-Philipp Machtens Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Pressure Question
On Thu, Nov 6, 2014 at 12:39 PM, Johnny Lu johnny.lu...@gmail.com wrote: I was not offended by the suggestion. With a sufficiently large number of water molecules, the protein would behave in the same way, under all three ensembles. Barostat and thermostat are artificial in some way. Biochemistry takes place in the NPT ensemble... NVT and NPT are different from NVE, but that doesn't make them artificial. Implementing such algorithms correctly is more tricky, however. At least, even the diffusion coefficient is different in a force field paper that used both NVE and NVT. Langevin thermostat destroys some momentum transfer. This is my first paper, and I don't know if the reviewer will be fine if I report that my simulation has an average pressure of 11 bar with error 0.5 bar. That would concern me, slightly more than the fact that you have a single simulation upon which to draw conclusions. Average pressure 1 in a fixed-volume ensemble means the system wants to change volume (get larger? I forget the convention). Why not do some NPT to find a volume it presumably likes better, and do another run? If the results are different, then you need more runs to find out what's going on. If the results are the same, then you've added weight to your conclusions. Mark On Thu, Nov 6, 2014 at 5:34 AM, Téletchéa Stéphane stephane.teletc...@univ-nantes.fr wrote: Le 06/11/2014 06:16, Antonio Baptista a écrit : In particular, the virial-based instantaneous pressure (call it P') computed in simulations has its ensemble average equal to the thermodynamic pressure P (check any good book on molecular simulation). But, as others already pointed out, this P' is well-known to show extremelly large fluctuations, meaning that its average computed from the simulation has usually a very large statistical spread. In other words, although the ensemble average of P' is strictly equal to P, its simulation average is a random variable that often shows large deviations from P (especially for short simulations). To get an idea of what is an acceptable error for the average of P', you may look at its distribution histogram in the NPT simulation. Dear Antonio, Sorry if my message sound aggressive when I talked about totally irrevelevant, I will clarify my thoughts. From a theoretical point of view, you are right, each ensemble is accessible. From a biological point of view, though, the concept of fixing the volume is less reasonable: we live at constant pressure and temperature, and also at tighly controlled pH, and salt concentrations. The volume varies though, as you feel it when the weather is getting hot or cold. My point was exactly what your are telling in a more formal way than me: this P' is well-known to show extremely large fluctuations Well, digging a bit more on my feeling, I also found opposite arguments on the AMBER mailing list, like here: http://archive.ambermd.org/201103/0431.html So I'll got back again on my research and adjust my mind on the actual bleeding edge simulations taking into account all the recent code and force fields progresses. Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.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.
[gmx-users] Avg. Volume in NPT by Small Coupling Time
Hi. How to get an accurate average volume for a system, such that the pressure will be at 1 bar in a subsequent NVT run using this average volume? Is it ok to use Berendsen barostat with a very small time constant (0.2 ps) ? (At first I picked 0.1ps, gromacs 4.6.7 told me to use at least 0.2 ps). I was hoping that a smaller time constant would allow the simulation to sample the volume more frequently and Berendsen barostat would help the system to converge to the correct average volume faster. What are the possible draw backs? So far (2 ns), I see that the pressure fluctuation is smaller than a PR barostat. It seems to be fine to use Berendsen barostat for this purpose ( [ https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-February/058453.html] ) Thank you again. -- 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] Pressure Question
Hi, Note that using the Berendsen thermostat in Gromacs adds defects for no gain, compared with the Bussi v-rescale thermostat. The latter *is* Berendsen, plus a stochastic term that produces the right energy and velocity distributions (unlike Berendsen). I'd give serious consideration to rejecting a paper that used Gromacs and the Berendsen thermostat, particularly if they did not discuss why the known defects of Berendsen were acceptable for their work. Mark On Thu, Nov 6, 2014 at 4:18 PM, Johnny Lu johnny.lu...@gmail.com wrote: That post in the amber mailing list was quite interesting. May be using a weak berendsen thermostat in NVT is fine for them. Thanks for sharing that. On Thu, Nov 6, 2014 at 6:39 AM, Johnny Lu johnny.lu...@gmail.com wrote: I was not offended by the suggestion. With a sufficiently large number of water molecules, the protein would behave in the same way, under all three ensembles. Barostat and thermostat are artificial in some way. At least, even the diffusion coefficient is different in a force field paper that used both NVE and NVT. Langevin thermostat destroys some momentum transfer. This is my first paper, and I don't know if the reviewer will be fine if I report that my simulation has an average pressure of 11 bar with error 0.5 bar. On Thu, Nov 6, 2014 at 5:34 AM, Téletchéa Stéphane stephane.teletc...@univ-nantes.fr wrote: Le 06/11/2014 06:16, Antonio Baptista a écrit : In particular, the virial-based instantaneous pressure (call it P') computed in simulations has its ensemble average equal to the thermodynamic pressure P (check any good book on molecular simulation). But, as others already pointed out, this P' is well-known to show extremelly large fluctuations, meaning that its average computed from the simulation has usually a very large statistical spread. In other words, although the ensemble average of P' is strictly equal to P, its simulation average is a random variable that often shows large deviations from P (especially for short simulations). To get an idea of what is an acceptable error for the average of P', you may look at its distribution histogram in the NPT simulation. Dear Antonio, Sorry if my message sound aggressive when I talked about totally irrevelevant, I will clarify my thoughts. From a theoretical point of view, you are right, each ensemble is accessible. From a biological point of view, though, the concept of fixing the volume is less reasonable: we live at constant pressure and temperature, and also at tighly controlled pH, and salt concentrations. The volume varies though, as you feel it when the weather is getting hot or cold. My point was exactly what your are telling in a more formal way than me: this P' is well-known to show extremely large fluctuations Well, digging a bit more on my feeling, I also found opposite arguments on the AMBER mailing list, like here: http://archive.ambermd.org/201103/0431.html So I'll got back again on my research and adjust my mind on the actual bleeding edge simulations taking into account all the recent code and force fields progresses. Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.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] Avg. Volume in NPT by Small Coupling Time
Hi, I think that's fine for rapidly forcing the volume to be close to the right equilibrium value, with low fluctuations. Then switch to gentler NPT (or constant-volume) for making a proper observation of the pressure. Mark On Thu, Nov 6, 2014 at 4:44 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. How to get an accurate average volume for a system, such that the pressure will be at 1 bar in a subsequent NVT run using this average volume? Is it ok to use Berendsen barostat with a very small time constant (0.2 ps) ? (At first I picked 0.1ps, gromacs 4.6.7 told me to use at least 0.2 ps). I was hoping that a smaller time constant would allow the simulation to sample the volume more frequently and Berendsen barostat would help the system to converge to the correct average volume faster. What are the possible draw backs? So far (2 ns), I see that the pressure fluctuation is smaller than a PR barostat. It seems to be fine to use Berendsen barostat for this purpose ( [ https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-February/058453.html ] ) Thank you again. -- 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] Pressure Question
I see. I'm using the V-rescaling thermostat in all simulations that I ran. I don't think I will use NPT for production run. I'm trying to get NVE production run in the end. If I use NVT production run, I will try to account for the effect of the thermostat (I'm not sure I can do that very well). On Thu, Nov 6, 2014 at 10:47 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Note that using the Berendsen thermostat in Gromacs adds defects for no gain, compared with the Bussi v-rescale thermostat. The latter *is* Berendsen, plus a stochastic term that produces the right energy and velocity distributions (unlike Berendsen). I'd give serious consideration to rejecting a paper that used Gromacs and the Berendsen thermostat, particularly if they did not discuss why the known defects of Berendsen were acceptable for their work. Mark On Thu, Nov 6, 2014 at 4:18 PM, Johnny Lu johnny.lu...@gmail.com wrote: That post in the amber mailing list was quite interesting. May be using a weak berendsen thermostat in NVT is fine for them. Thanks for sharing that. On Thu, Nov 6, 2014 at 6:39 AM, Johnny Lu johnny.lu...@gmail.com wrote: I was not offended by the suggestion. With a sufficiently large number of water molecules, the protein would behave in the same way, under all three ensembles. Barostat and thermostat are artificial in some way. At least, even the diffusion coefficient is different in a force field paper that used both NVE and NVT. Langevin thermostat destroys some momentum transfer. This is my first paper, and I don't know if the reviewer will be fine if I report that my simulation has an average pressure of 11 bar with error 0.5 bar. On Thu, Nov 6, 2014 at 5:34 AM, Téletchéa Stéphane stephane.teletc...@univ-nantes.fr wrote: Le 06/11/2014 06:16, Antonio Baptista a écrit : In particular, the virial-based instantaneous pressure (call it P') computed in simulations has its ensemble average equal to the thermodynamic pressure P (check any good book on molecular simulation). But, as others already pointed out, this P' is well-known to show extremelly large fluctuations, meaning that its average computed from the simulation has usually a very large statistical spread. In other words, although the ensemble average of P' is strictly equal to P, its simulation average is a random variable that often shows large deviations from P (especially for short simulations). To get an idea of what is an acceptable error for the average of P', you may look at its distribution histogram in the NPT simulation. Dear Antonio, Sorry if my message sound aggressive when I talked about totally irrevelevant, I will clarify my thoughts. From a theoretical point of view, you are right, each ensemble is accessible. From a biological point of view, though, the concept of fixing the volume is less reasonable: we live at constant pressure and temperature, and also at tighly controlled pH, and salt concentrations. The volume varies though, as you feel it when the weather is getting hot or cold. My point was exactly what your are telling in a more formal way than me: this P' is well-known to show extremely large fluctuations Well, digging a bit more on my feeling, I also found opposite arguments on the AMBER mailing list, like here: http://archive.ambermd.org/201103/0431.html So I'll got back again on my research and adjust my mind on the actual bleeding edge simulations taking into account all the recent code and force fields progresses. Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.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
Re: [gmx-users] centering a protofibril in a box
Thanks Justin. I know it was not enough clear, it was because of my limited English proficiency. What I wanted (and want) to do is centering the first monomer of the protofibril in the box, so the protofibril would be shifted to the bottom part allowing aggregate more and more monomers without having to use a bigger box. But using this trjconv -f protofibril.pdb -n index.ndx -center -s protofibril.pdb -o test.pdb (index.ndx is an index I did for the residues corresponding to the first monomer and that is which I chose as select group for centering) what I get is that the center of the box matches with the center of the protofibril (looking at the longitudinal direction of the protofibril), as it doesnt care about the index. By the way, do you know why -s file.pdb is required? Maybe it is not possible to do what I want with this command; but it is just center the protofibril with respect to its first monomer. I will try with editconf instead. Thanks a lot for your time. Adriana *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ** 2014-11-06 13:54 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 11/6/14 6:13 AM, Adriana Garro wrote: Dear all, I am trying to center a protofibril in a box, but respect to its first monomer. (the result would be the protofibril shiftted to the botton of the box) I used trjconv -f protofibril.pdb -n index.ndx -center -s protofibril.pdb -o test.pdb I did an index for the residues corresponding to the first monomer and that is which I chose as select group for centering but when I visualize the System with vmd the protofibril appears in the center of the box but as it was just one molecule. You can accomplish this with either editconf -translate or trjconv -trans. I don't exactly know what's going on from your description - an image here would be good, because the last sentence doesn't make much sense to me. -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] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500
On Thu, Nov 6, 2014 at 4:35 PM, Machtens, Jan-Philipp j.macht...@fz-juelich.de wrote: Hi, yes I will post that to redmine soon, but let me first clarify the issue, since I tested some more conditions in the meantime. (I realized that my trajectory had 1501 frames and the error occured when I choose more than 500 atoms, i.e. when the number of degrees of freedom becomes larger then the number of frames). So in general, if your trajectory has nf frames, g_covar will result in a segfault if the group to be (covariance) analyzed is larger then nf/3 atoms. If found this statement to be true for gromacs 4.6.6, 4.6.7 and 5.0.2. This error does not happen for gromacs 4.6.5 So, I wonder whether this is an unwanted behaviour which has been introduced in 4.6.6? Do you think this behavior makes sense ? The official release notes for 4.6.6 do not mention changes in g_covar. Correct, but a change (git hash 972032bfb8) that was intended to fix a problem observed with g_anaeig also affected code in g_covar (which I have now corrected in the release notes). The nature of the change seems very consistent with your observations. Mark Best, Jan-Philipp Machtens From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: Thursday, November 06, 2014 1:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500 Hi, IIRC some minor bugs were fixed, but a regression like that should be dealt with... please file at http://redmine.gromacs.org. Mark On Thu, Nov 6, 2014 at 12:00 PM, Machtens, Jan-Philipp j.macht...@fz-juelich.de wrote: Dear all, I observed that g_covar in Gromacs 5.0.2 segfaults at the diagonalization step, if the group for the covariance analysis is bigger than 500 atoms, i.e. if the covariance matrix is bigger than 1500x1500. In my hands, this problem does not arise with g_covar 4.6.x. The results obtained from g_covar (version 5.x) on groups = 500 atoms that I obtained were the same os those from version 4.6.x and also verified manually. Memory is not the problem here. The problem is independent on single/double precision. Before posting this on redmine.gromacs I first want to check whether someone here has made a contradicting experience which would argue against a possible bug introduced in 5.0.2? Thanks. Cheers, Jan-Philipp Machtens Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Avg. Volume in NPT by Small Coupling Time
Assume sampling is sufficient in all stages of simulations. Will the berendsen barostat with this coupling constant give both the correct average volume and correct average pressure? (despite the distribution is not canonical) Will that average pressure change when I switch to NVT ensemble? Can I switch to NVT directly (without doing a NPT with PR barostat) for a while, and then finally go to NVE production run? (a nature communication paper did that, but didn't report the barostat coupling constant they used in the NPT simulation.) On Thu, Nov 6, 2014 at 10:51 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I think that's fine for rapidly forcing the volume to be close to the right equilibrium value, with low fluctuations. Then switch to gentler NPT (or constant-volume) for making a proper observation of the pressure. Mark On Thu, Nov 6, 2014 at 4:44 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. How to get an accurate average volume for a system, such that the pressure will be at 1 bar in a subsequent NVT run using this average volume? Is it ok to use Berendsen barostat with a very small time constant (0.2 ps) ? (At first I picked 0.1ps, gromacs 4.6.7 told me to use at least 0.2 ps). I was hoping that a smaller time constant would allow the simulation to sample the volume more frequently and Berendsen barostat would help the system to converge to the correct average volume faster. What are the possible draw backs? So far (2 ns), I see that the pressure fluctuation is smaller than a PR barostat. It seems to be fine to use Berendsen barostat for this purpose ( [ https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-February/058453.html ] ) Thank you again. -- 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] Pressure Question
If the problem of using a 11 bar simulation is as big as the problem of drawing conclusion from a single simulation, I guess I have to get a pressure closer to 1 bar. Thanks. On Thu, Nov 6, 2014 at 10:55 AM, Johnny Lu johnny.lu...@gmail.com wrote: I see. I'm using the V-rescaling thermostat in all simulations that I ran. I don't think I will use NPT for production run. I'm trying to get NVE production run in the end. If I use NVT production run, I will try to account for the effect of the thermostat (I'm not sure I can do that very well). On Thu, Nov 6, 2014 at 10:47 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Note that using the Berendsen thermostat in Gromacs adds defects for no gain, compared with the Bussi v-rescale thermostat. The latter *is* Berendsen, plus a stochastic term that produces the right energy and velocity distributions (unlike Berendsen). I'd give serious consideration to rejecting a paper that used Gromacs and the Berendsen thermostat, particularly if they did not discuss why the known defects of Berendsen were acceptable for their work. Mark On Thu, Nov 6, 2014 at 4:18 PM, Johnny Lu johnny.lu...@gmail.com wrote: That post in the amber mailing list was quite interesting. May be using a weak berendsen thermostat in NVT is fine for them. Thanks for sharing that. On Thu, Nov 6, 2014 at 6:39 AM, Johnny Lu johnny.lu...@gmail.com wrote: I was not offended by the suggestion. With a sufficiently large number of water molecules, the protein would behave in the same way, under all three ensembles. Barostat and thermostat are artificial in some way. At least, even the diffusion coefficient is different in a force field paper that used both NVE and NVT. Langevin thermostat destroys some momentum transfer. This is my first paper, and I don't know if the reviewer will be fine if I report that my simulation has an average pressure of 11 bar with error 0.5 bar. On Thu, Nov 6, 2014 at 5:34 AM, Téletchéa Stéphane stephane.teletc...@univ-nantes.fr wrote: Le 06/11/2014 06:16, Antonio Baptista a écrit : In particular, the virial-based instantaneous pressure (call it P') computed in simulations has its ensemble average equal to the thermodynamic pressure P (check any good book on molecular simulation). But, as others already pointed out, this P' is well-known to show extremelly large fluctuations, meaning that its average computed from the simulation has usually a very large statistical spread. In other words, although the ensemble average of P' is strictly equal to P, its simulation average is a random variable that often shows large deviations from P (especially for short simulations). To get an idea of what is an acceptable error for the average of P', you may look at its distribution histogram in the NPT simulation. Dear Antonio, Sorry if my message sound aggressive when I talked about totally irrevelevant, I will clarify my thoughts. From a theoretical point of view, you are right, each ensemble is accessible. From a biological point of view, though, the concept of fixing the volume is less reasonable: we live at constant pressure and temperature, and also at tighly controlled pH, and salt concentrations. The volume varies though, as you feel it when the weather is getting hot or cold. My point was exactly what your are telling in a more formal way than me: this P' is well-known to show extremely large fluctuations Well, digging a bit more on my feeling, I also found opposite arguments on the AMBER mailing list, like here: http://archive.ambermd.org/201103/0431.html So I'll got back again on my research and adjust my mind on the actual bleeding edge simulations taking into account all the recent code and force fields progresses. Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.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
Re: [gmx-users] problem in NPT equilibration
Dear Justin, Thanks for the clarification. I am currently doing the NVT step and after that I will move forward to the production md run. Regards, Soumadwip -- 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] help for strange linear force in Pulling
Dear Gromacs User, I am using the pulling to pull two objects apart with Gomacs 4.6.5. To avoid the issues of half-box size limitation, i used direction_periodic to make two objects apart from each more than half-box-size distance. I just got the linear force: force change with time linearly. This is wrong. I don't know for the following setting gmx gives linear force. -- pull = umbrella pull_geometry= direction_periodic pull_dim = Y Y Y pull_start = yes ; define initial COM distance 0 pull_ngroups = 1 pull_group0 = P1 pull_group1 = P2 pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 500 ; kJ mol^-1 nm^-2 -- this is the from pullf.xvg: - # mdrun_mpi is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat @title Pull force @xaxis label Time (ps) @yaxis label Force (kJ/mol/nm) @TYPE xy 0. -0 0.0010 0.0001 0.0020 0.0002 0.0030 0.0003 0.0040 0.0004 0.0050 0.0005 0.0060 0.0006 0.0070 0.0007 --- If I switch pull_geometry = direction, the result makes sense. there would be no linear force. Thanks a lot for the help! Thomas -- 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] Frequency dependent dielectric constant
Hello, It's a friendly reminder if someone knows how to calculate. Please let me know. Thank you. Bharat -- 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] Frequency dependent dielectric constant
On 2014-11-06 19:33, Bharat Sharma wrote: Hello, It's a friendly reminder if someone knows how to calculate. Please let me know. g_dielectric. Thank you. Bharat -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 exclude atoms within the same molecule from an rdf.
I'm simulating a mixture of molecules (call them Molecules A, B, and C). The rdf between A and B and between A and C both look fine, but the one between A and A is crazy-looking. I assume this is because it's comparing atoms within the same molecule. I can't figure out how to exclude atoms in the same molecule from the rdf. Thanks, Stella -- 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] Fwd: Re: Frequency dependent dielectric constant
Original Message Subject:Re: [gmx-users] Frequency dependent dielectric constant Date: Thu, 6 Nov 2014 16:23:34 -0500 From: Bharat Sharma bharatsolbri...@gmail.com To: sp...@xray.bmc.uu.se Hello Professor David, Sorry for sending you a private email. Thank you for your reply on forum. Is it possible to use external dipole moment file which has t Mx My Mz data to calculate autocorrelation function which is defined as phi (t) = M(t). M(o)/ M(0)^2. Autocorrelation file is necessary to use g_dielectric function. Thank you. Sincerely, Bharat Sharma I have a file like this. 1 -18.4054002593869 -8.63550624406573 13.1822307410726 2 -16.3448281386543 -9.26825538523777 12.6970594193942 3 -16.2122319636283 -9.584079278168 10.1880749346946 4 -16.8000261232119 -9.3544161158981 9.292811661397 5 -16.9675609841484 -8.06386828149236 9.04336117783739 6 -16.705420659386 -8.15253302392368 6.35375835558321 7 -16.3482274903309 -7.42833201686778 2.40403368273462 8 -17.6089611732605 -6.5810524629 1.0191769956 9 -19.1340573022822 -7.31608247201016 1.0593505375146 10 -18.8898972984193 -8.50162965184524 -0.390241915321422 11 -17.3201971209895 -8.88827721892198 -2.91666461388975 12 -17.9697387584415 -10.3820791259894 -3.09327709524195 13 -19.4150366450719 -12.5922697307389 -1.76640044899152 14 -17.2192770802751 -12.719093017379 -1.76633521518987 15 -13.9887596873511 -11.6333686786579 -2.53760673124873 16 -15.631174760539 -11.8671822022606 -1.04251159658716 17 -19.7752453695527 -13.1793702340658 0.669842005269544 18 -20.5031312769212 -12.8221354246758 1.7010916111 19 -20.1714747689171 -11.5235359847683 3.12874014505405 20 -23.4993319248317 -11.1069526872016 5.40262656219366 21 -26.9810468267155 -10.3960073112131 6.66596873251908 22 -25.2970021256126 -8.26285916407095 6.85639239972755 23 -22.3727114023644 -7.29618209094124 7.96149529066325 24 -22.8378886264605 -7.94207228198017 9.4631219697683 25 -23.9479347882939 -8.18332794071831 8.90226933404197 26 -23.4431023794441 -8.57868882479158 7.48452761101869 27 -23.8923601075312 -9.80575680710948 7.74832733959732 28 -26.2650526524463 -11.6213772988559 7.80737869303804 29 -28.726262739164 -11.5765264683748 3.98968339600384 30 -28.8118374367959 -10.5568670286443 1.98998557532743 On Thu, Nov 6, 2014 at 2:08 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2014-11-06 19:33, Bharat Sharma wrote: Hello, It's a friendly reminder if someone knows how to calculate. Please let me know. g_dielectric. Thank you. Bharat -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205 tel:%2B46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/GMX-__Users_List http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/__mailman/listinfo/gromacs.org___gmx-users https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org mailto: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 exclude atoms within the same molecule from an rdf.
It's fairly simple: generate a .tpr file with a nrexcl big enough to exclude self-counts and give it to g_rdf through the -s flag. João On Thu, Nov 6, 2014 at 8:42 PM, Stella Nickerson stella.nicker...@gmail.com wrote: I'm simulating a mixture of molecules (call them Molecules A, B, and C). The rdf between A and B and between A and C both look fine, but the one between A and A is crazy-looking. I assume this is because it's comparing atoms within the same molecule. I can't figure out how to exclude atoms in the same molecule from the rdf. Thanks, Stella -- 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. -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- 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] Fwd: Re: Frequency dependent dielectric constant
On 2014-11-06 22:28, David van der Spoel wrote: Original Message Subject: Re: [gmx-users] Frequency dependent dielectric constant Date: Thu, 6 Nov 2014 16:23:34 -0500 From: Bharat Sharma bharatsolbri...@gmail.com To: sp...@xray.bmc.uu.se Hello Professor David, Sorry for sending you a private email. Thank you for your reply on forum. Is it possible to use external dipole moment file which has t Mx My Mz data to calculate autocorrelation function which is defined as phi (t) = M(t). M(o)/ M(0)^2. Autocorrelation file is necessary to use g_dielectric function. Looks like you have not run gmx dielectric -h You need the acf which you can produce using gmx dipoles Thank you. Sincerely, Bharat Sharma I have a file like this. 1 -18.4054002593869 -8.63550624406573 13.1822307410726 2 -16.3448281386543 -9.26825538523777 12.6970594193942 3 -16.2122319636283 -9.584079278168 10.1880749346946 4 -16.8000261232119 -9.3544161158981 9.292811661397 5 -16.9675609841484 -8.06386828149236 9.04336117783739 6 -16.705420659386 -8.15253302392368 6.35375835558321 7 -16.3482274903309 -7.42833201686778 2.40403368273462 8 -17.6089611732605 -6.5810524629 1.0191769956 9 -19.1340573022822 -7.31608247201016 1.0593505375146 10 -18.8898972984193 -8.50162965184524 -0.390241915321422 11 -17.3201971209895 -8.88827721892198 -2.91666461388975 12 -17.9697387584415 -10.3820791259894 -3.09327709524195 13 -19.4150366450719 -12.5922697307389 -1.76640044899152 14 -17.2192770802751 -12.719093017379 -1.76633521518987 15 -13.9887596873511 -11.6333686786579 -2.53760673124873 16 -15.631174760539 -11.8671822022606 -1.04251159658716 17 -19.7752453695527 -13.1793702340658 0.669842005269544 18 -20.5031312769212 -12.8221354246758 1.7010916111 19 -20.1714747689171 -11.5235359847683 3.12874014505405 20 -23.4993319248317 -11.1069526872016 5.40262656219366 21 -26.9810468267155 -10.3960073112131 6.66596873251908 22 -25.2970021256126 -8.26285916407095 6.85639239972755 23 -22.3727114023644 -7.29618209094124 7.96149529066325 24 -22.8378886264605 -7.94207228198017 9.4631219697683 25 -23.9479347882939 -8.18332794071831 8.90226933404197 26 -23.4431023794441 -8.57868882479158 7.48452761101869 27 -23.8923601075312 -9.80575680710948 7.74832733959732 28 -26.2650526524463 -11.6213772988559 7.80737869303804 29 -28.726262739164 -11.5765264683748 3.98968339600384 30 -28.8118374367959 -10.5568670286443 1.98998557532743 On Thu, Nov 6, 2014 at 2:08 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2014-11-06 19:33, Bharat Sharma wrote: Hello, It's a friendly reminder if someone knows how to calculate. Please let me know. g_dielectric. Thank you. Bharat -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205 tel:%2B46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/GMX-__Users_List http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/__mailman/listinfo/gromacs.org___gmx-users https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Umbrella sampling ignore hydrogen command -ignh
I am trying to perform a simulation regarding the effect that hydration has on tensile response for my system. When i looked into the umbrella sampling tutorial it said to create a start file using the pdb2gmx -f input.pdb -ignh -ter -o complex.gro command and was wondering what effect that the -ignh option had on my simulated results? do the hydrogens not get accounted for in this simulation, and if so, how are the atomic bonds in which the hydrogens are supposed to be located treated in terms of replacing those hydrogens? does this mean i am doing a united atom model ? *The simplicity of nature is not to be measured by that of our conceptions. Infinitely varied in its effects, nature is simple only in its causes, and its economy consists in producing a great number of phenomena, often very complicated, by means of a small number of general laws.* *--Pierre Simon de Laplace* -- 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] Version problem
can look for all files with name mdrun by $ find / -name mdrun * mdrun_search and then $ cat mdrun_search On Thu, Nov 6, 2014 at 7:25 AM, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Hi, 'which mdrun' only tells you the location of the mdrun you're currently using and is no good here. How did you install 5.0.2? The CMake files should tell you where installation directory is. Kind regards, Erik On 6 Nov 2014, at 11:43, sa...@physics.iisc.ernet.in wrote: tried which mdrun showing the path /usr/bin/mdrun, which v4.6.5, however I have downloaded v5.0.2.tar.gz and used for installation. try to find mdrun program by typing this command on terminal: which mdrun will show path of mdrun program where it located. On Nov 6, 2014 4:01 PM, sa...@physics.iisc.ernet.in wrote: Dear Dr. Carsten Kutzner, I am unable to find the gmx5/bin/GMXRC in my machine, used 'locate' and 'find' to search the location. However I have source the following: source /usr/share/gromacs/shell-specific/GMXRC.bashrc Without this also mdrun is running. I am definitely missing something. Kindly help. With best regards, Satya On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote: Dear all, I am new to GROMACS, just finish installation of v5.0.2, started reading online manual, as instructed executed the command: mdrun -version and the printout pasted below. It is printing GROMACS version 4.6.5, however I have installed version 5.0.2. What is the problem? Find the directory to where you have installed your GROMACS 5.0 executables and then do source /path/to/gmx5/bin/GMXRC which mdrun should now give you the 5.0 mdrun Carsten Regards, Satyabrata Das == Program: mdrun Gromacs version:VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Sun Dec 15 04:01:11 UTC 2013 Built by: buildd@panlong [CMAKE] Build OS/arch: Linux 3.2.0-37-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5620 @ 2.40GHz Build CPU family: 6 Model: 44 Stepping: 2 Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2 C compiler flags: -msse4.1-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG satyabrata@satyabrata-desktop:~$ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] Version problem
I typed an extra space that shouldn't be there. $ find / -name mdrun* mdrun_search On Thu, Nov 6, 2014 at 5:03 PM, Johnny Lu johnny.lu...@gmail.com wrote: can look for all files with name mdrun by $ find / -name mdrun * mdrun_search and then $ cat mdrun_search On Thu, Nov 6, 2014 at 7:25 AM, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Hi, 'which mdrun' only tells you the location of the mdrun you're currently using and is no good here. How did you install 5.0.2? The CMake files should tell you where installation directory is. Kind regards, Erik On 6 Nov 2014, at 11:43, sa...@physics.iisc.ernet.in wrote: tried which mdrun showing the path /usr/bin/mdrun, which v4.6.5, however I have downloaded v5.0.2.tar.gz and used for installation. try to find mdrun program by typing this command on terminal: which mdrun will show path of mdrun program where it located. On Nov 6, 2014 4:01 PM, sa...@physics.iisc.ernet.in wrote: Dear Dr. Carsten Kutzner, I am unable to find the gmx5/bin/GMXRC in my machine, used 'locate' and 'find' to search the location. However I have source the following: source /usr/share/gromacs/shell-specific/GMXRC.bashrc Without this also mdrun is running. I am definitely missing something. Kindly help. With best regards, Satya On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote: Dear all, I am new to GROMACS, just finish installation of v5.0.2, started reading online manual, as instructed executed the command: mdrun -version and the printout pasted below. It is printing GROMACS version 4.6.5, however I have installed version 5.0.2. What is the problem? Find the directory to where you have installed your GROMACS 5.0 executables and then do source /path/to/gmx5/bin/GMXRC which mdrun should now give you the 5.0 mdrun Carsten Regards, Satyabrata Das == Program: mdrun Gromacs version:VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Sun Dec 15 04:01:11 UTC 2013 Built by: buildd@panlong [CMAKE] Build OS/arch: Linux 3.2.0-37-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5620 @ 2.40GHz Build CPU family: 6 Model: 44 Stepping: 2 Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2 C compiler flags: -msse4.1-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG satyabrata@satyabrata-desktop:~$ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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
Re: [gmx-users] centering a protofibril in a box
On 11/6/14 10:58 AM, Adriana Garro wrote: Thanks Justin. I know it was not enough clear, it was because of my limited English proficiency. What I wanted (and want) to do is centering the first monomer of the protofibril in the box, so the protofibril would be shifted to the bottom part allowing aggregate more and more monomers without having to use a bigger box. But using this trjconv -f protofibril.pdb -n index.ndx -center -s protofibril.pdb -o test.pdb (index.ndx is an index I did for the residues corresponding to the first monomer and that is which I chose as select group for centering) what I get is that the center of the box matches with the center of the protofibril (looking at the longitudinal direction of the protofibril), as it doesnt care about the index. I suppose it depends on the dimensions of the box as defined in the .pdb file. By the way, do you know why -s file.pdb is required? In general, it depends on what you're actually doing. The information in -s may be used for box information, masses, atom/residue names, etc. In this case, trjconv needs names. Any time you want to write a coordinate file, you need to supply a suitable input for -s. Maybe it is not possible to do what I want with this command; but it is just center the protofibril with respect to its first monomer. I will try with editconf instead. That would likely be easiest. Extract the COM coordinates using g_traj, then you know exactly how much you need to translate the structure. -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] Umbrella sampling ignore hydrogen command -ignh
On 11/6/14 4:53 PM, Chris Papamitrou wrote: I am trying to perform a simulation regarding the effect that hydration has on tensile response for my system. When i looked into the umbrella sampling tutorial it said to create a start file using the pdb2gmx -f input.pdb -ignh -ter -o complex.gro command and was wondering what effect that the -ignh option had on my simulated results? do the hydrogens not get accounted for in this simulation, and if so, how are the atomic bonds in which the hydrogens are supposed to be located treated in terms of replacing those hydrogens? does this mean i am doing a united atom model ? Start with pdb2gmx -h. The -ignh has a very simple purpose, and it's used mostly for working around nomenclature issues. Whether or not you use a united-atom force field is entirely up to you, based on what you choose. -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] Pressure Question
On Thu, 6 Nov 2014, Téletchéa Stéphane wrote: Le 06/11/2014 06:16, Antonio Baptista a écrit : In particular, the virial-based instantaneous pressure (call it P') computed in simulations has its ensemble average equal to the thermodynamic pressure P (check any good book on molecular simulation). But, as others already pointed out, this P' is well-known to show extremelly large fluctuations, meaning that its average computed from the simulation has usually a very large statistical spread. In other words, although the ensemble average of P' is strictly equal to P, its simulation average is a random variable that often shows large deviations from P (especially for short simulations). To get an idea of what is an acceptable error for the average of P', you may look at its distribution histogram in the NPT simulation. Dear Antonio, Sorry if my message sound aggressive when I talked about totally irrevelevant, I will clarify my thoughts. No problem, Stéphane. I was just trying to avoid propagating the wrong idea that a parameter is irrelevant in an ensemble where its value is not explicitly imposed, an idea I saw stated before in several discussions. Anyway, it seems I misunderstood you, since you say you were actually making the same point... :) Best, Antonio From a theoretical point of view, you are right, each ensemble is accessible. From a biological point of view, though, the concept of fixing the volume is less reasonable: we live at constant pressure and temperature, and also at tighly controlled pH, and salt concentrations. The volume varies though, as you feel it when the weather is getting hot or cold. My point was exactly what your are telling in a more formal way than me: this P' is well-known to show extremely large fluctuations Well, digging a bit more on my feeling, I also found opposite arguments on the AMBER mailing list, like here: http://archive.ambermd.org/201103/0431.html So I'll got back again on my research and adjust my mind on the actual bleeding edge simulations taking into account all the recent code and force fields progresses. Best, Stéphane -- Team Protein Design In Silico UFIP, UMR 6286 CNRS, UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.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] Charmm to gromacs conversion for lipids
Dear Justin, Please check the atom section of toppar_all36_lipid_cholesterol.str file that I pasted below. * Toppar stream file for cholesterol. Stream following reading of * top_all36_lipid.rtf and par_all36_lipid.rtf !reference !Suits, F., Pitman, M., MacKerell, A.D., Jr., Feller, S.E. Molecular Level !Organization of Saturated and Polyunsaturated Fatty Acids in a !Phosphatidylcholine Bilayer Containing Cholesterol Submitted !for publication read rtf card append * cholesterol residues * RESI CHL1 0.00 !cholesterol (name to avoid conflict with choline) ! atoms names correspond to the correct cholesterol nomenclature GROUP ATOM C3 CTL1 0.14 ATOM O3 OHL -0.66 ATOM H3' HOL 0.43 ATOM H3 HAL1 0.09 GROUP ATOM C4 CTL2-0.18 ATOM H4A HAL2 0.09 ATOM H4B HAL2 0.09 GROUP ATOM C5 CEL1 0.00 ATOM C6 CEL1-0.15 ATOM H6 HEL1 0.15 GROUP ATOM C7 CTL2-0.18 ATOM H7A HAL2 0.09 ATOM H7B HAL2 0.09 GROUP ATOM C8 CTL1-0.09 ATOM H8 HAL1 0.09 GROUP ATOM C14 CTL1-0.09 ATOM H14 HAL1 0.09 GROUP ATOM C15 CTL2-0.18 ATOM H15A HAL2 0.09 ATOM H15B HAL2 0.09 GROUP ATOM C16 CTL2-0.18 ATOM H16A HAL2 0.09 ATOM H16B HAL2 0.09 GROUP ATOM C17 CTL1-0.09 ATOM H17 HAL1 0.09 GROUP ATOM C13 CTL1 0.00 GROUP ATOM C18 CTL3-0.27 !methyl at c13 ATOM H18A HAL3 0.09 ATOM H18B HAL3 0.09 ATOM H18C HAL3 0.09 GROUP ATOM C12 CTL2-0.18 ATOM H12A HAL2 0.09 ATOM H12B HAL2 0.09 GROUP ATOM C11 CTL2-0.18 ATOM H11A HAL2 0.09 ATOM H11B HAL2 0.09 GROUP ATOM C9 CTL1-0.09 ATOM H9 HAL1 0.09 GROUP ATOM C10 CTL1 0.00 GROUP ATOM C19 CTL3-0.27 !methyl at c10 ATOM H19A HAL3 0.09 ATOM H19B HAL3 0.09 ATOM H19C HAL3 0.09 GROUP ATOM C1 CTL2-0.18 ATOM H1A HAL2 0.09 ATOM H1B HAL2 0.09 GROUP ATOM C2 CTL2-0.18 ATOM H2A HAL2 0.09 ATOM H2B HAL2 0.09 GROUP ATOM C20 CTL2-0.09 ATOM H20 HAL2 0.09 GROUP ATOM C21 CTL3-0.27 ATOM H21A HAL3 0.09 ATOM H21B HAL3 0.09 ATOM H21C HAL3 0.09 GROUP ATOM C22 CTL2-0.18 ATOM H22A HAL2 0.09 ATOM H22B HAL2 0.09 GROUP ATOM C23 CTL2-0.18 ATOM H23A HAL2 0.09 ATOM H23B HAL2 0.09 GROUP ATOM C24 CTL2-0.18 !beyond this nomenclature may not be correct ATOM H24A HAL2 0.09 ATOM H24B HAL2 0.09 GROUP ATOM C25 CTL1-0.09 !c25 ATOM H25 HAL1 0.09 GROUP ATOM C26 CTL3-0.27 !terminal methyl, c26 ATOM H26A HAL3 0.09 ATOM H26B HAL3 0.09 ATOM H26C HAL3 0.09 GROUP ATOM C27 CTL3-0.27 !terminal methyl, c27 ATOM H27A HAL3 0.09 ATOM H27B HAL3 0.09 ATOM H27C HAL3 0.09 On Thu, Nov 6, 2014 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/6/14 8:38 AM, Venkat Reddy wrote: Dear Justin, Yes, the problem is with the blank line at the end of atomtypes.atp. Now its working fine. I have added the missing dihedral types from other sources. Thanks, I will fix that. I have compared the cholesterol CHARMM parameters that are converted to gromacs format and original parameters from toppar_all36_lipid_cholesterol.str file available in CHARMM website. I found some variations in the atom types. For eg., The atom type of C3 atom from sterol ring in cholesterol is CTL1 in CHARMM whereas it is CG311 in charmm36-Nov2014.ff. Which residue are you looking at? There is no C3 atom with type CTL1 in that stream file. In any case, CG311 and CTL1 have identical parameters (see ffnonbonded.itp) since CG311 is used for CGenFF model compounds, which in the case of lipids, were just ported over and given unique types. Anything with a G as the second letter in the atom type is from CGenFF, indicating general to differentiate them from the main CHARMM types. -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. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions
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Re: [gmx-users] centering a protofibril in a box
Hi Adriana, Centering only shifts the positions. I guess you also want to put stuff back into the box and then make the molecules whole. You'll probably need several passes to get what you want. Cheers, Tsjerk On Nov 6, 2014 11:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/6/14 10:58 AM, Adriana Garro wrote: Thanks Justin. I know it was not enough clear, it was because of my limited English proficiency. What I wanted (and want) to do is centering the first monomer of the protofibril in the box, so the protofibril would be shifted to the bottom part allowing aggregate more and more monomers without having to use a bigger box. But using this trjconv -f protofibril.pdb -n index.ndx -center -s protofibril.pdb -o test.pdb (index.ndx is an index I did for the residues corresponding to the first monomer and that is which I chose as select group for centering) what I get is that the center of the box matches with the center of the protofibril (looking at the longitudinal direction of the protofibril), as it doesnt care about the index. I suppose it depends on the dimensions of the box as defined in the .pdb file. By the way, do you know why -s file.pdb is required? In general, it depends on what you're actually doing. The information in -s may be used for box information, masses, atom/residue names, etc. In this case, trjconv needs names. Any time you want to write a coordinate file, you need to supply a suitable input for -s. Maybe it is not possible to do what I want with this command; but it is just center the protofibril with respect to its first monomer. I will try with editconf instead. That would likely be easiest. Extract the COM coordinates using g_traj, then you know exactly how much you need to translate the structure. -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.
[gmx-users] smd
Dear everyone， i want to use gromacs to perform the steered molecular dynamcs simulation. My system is the protein-ligand complex in the center of the box an i want to pull out of the ligand form the protein ative site. i have set the pbc in my mdp file. However, after simulation, i find that the ligand out of the box and get into the next unit cell. How does this make sense? should i the box larger to keep the liand in the original unit cell? -- 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.
