[gmx-users] Re: Re: question about trjcat command: Merge files
Dear community. Thanks to all, finally I could resolve my problem, with the option -setttime, it was vital, then c (continue). Now I have two questions, 1) In which case the option l could be useful? I did not understand very well the aplicability. 2) Could you please recommend me an article (Most cited maybe) or tutorial that analyze changes in protein folding due to single mutation? I would like to study its methodology. Thanks in advance. Miguel. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] question about trajcat command: Merge files
Dear community, I have a couple of doubts, please help me to clarify. I performed 4 MD simulations using Gromacs (each one of 1ns, 2ns, 3ns ,4ns) , they are only a continuation of the last, because of I was explored the rmsd variation along the time. Now I want to merge all the trajectories to do only one plot of 10ns. So, I did: trajcat -f md_1ns_noPBC.xtc md_2ns_noPBC.xtc md_3ns_noPBC.xtc md_4ns_noPBC.xtc -o TOTAL_10ns_noPBC.xtc The program showed this: FileStart time Time step - md_1ns_noPBC.xtc0.000 ps2.000 ps md_2ns_noPBC.xtc0.000 ps2.000 ps WARNING: same Start time as previous md_3ns_noPBC.xtc0.000 ps2.000 ps WARNING: same Start time as previous md_4ns_noPDB.xtc0.000 ps2.000 ps WARNING: same Start time as previous I am worry about the message 'WARNING: same Start time as previous', I think is normal because each simulation is like independent, that is the reason why start time is take as 0ps. Please tell me If my command line is correct according to my purposes. By the way, to make the plot (RMSD 10ns) I plan to do it with -s md_1ns.tpr, is it correct? Thank you in advance. Miguel Quiliano. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: question about trajcat command: Merge files
Dear Justin. Thank you for you answer. But, the case I wrote, it was an ideally case. To help anyone in the forum at the same time. As soon as I have read your answer I tried. In my case my simulations were: First simulation: 0.4ns Second : 1ns Third: 2ns Fourth: 10ns -- Total = 13.4ns So I planned to do an RMSD plot of 0-13.4ns. As I said before, each simulation is the continuation of the previous, obviously to do this I used checkpoint files for each simulation and the same MD.mdp, only changed the time of simulation. I did: trajcat -f md_0_4ns_noPBC.xtc md_1ns_noPBC.xtc md_2ns_noPBC.xtc md_10ns_noPBC.xtc -o TOTAL_13_4ns_noPBC.xtc Then for curiosity I did ls -lh rw-r--r-- 1 willy bioinfo 368M 2011-06-01 13:10 md_0_4_noPBC.xtc -rw-r--r-- 1 willy bioinfo 917M 2011-06-01 13:12 md_1ns_noPBC.xtc -rw-r--r-- 1 willy bioinfo 917M 2011-06-01 13:13 md_2ns_noPBC.xtc -rw-r--r-- 1 willy bioinfo 9.0G 2011-06-01 13:17 md_10ns_noPDB.xtc -rw-r--r-- 1 willy bioinfo 9.0G 2011-06-01 15:44 TOTAL_13_4ns_noPBC.xtc Surprisingly the file TOTAL_13_4ns_noPBC.xtc had the same size of the file md_10ns_noPDB.xtc, is it normal? Continue with the process, then: g_rms -s molecule_sol_ion_MD_0_4ns.tpr -f TOTAL_13_4ns_noPDB.xtc -o rmsd_13_4ns_molecule.xvg -tu ns I open the .XVG as a simple .txt and I noticed that the time only reach 10ns or 1ps. Why not 13.4ns? I would be very grateful If you can tell me what is happening. Thanks in adavance. Miguel Quiliano. 2011/6/1 gmx-users-requ...@gromacs.org Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: scaling non-bonded interactions (Da-Wei Li) 2. question about trajcat command: Merge files (Miguel Quiliano Meza) 3. Re: Re: scaling non-bonded interactions (Justin A. Lemkul) 4. Re: scaling non-bonded interactions (Justin A. Lemkul) 5. Re: question about trajcat command: Merge files (Justin A. Lemkul) 6. RE: Re: scaling non-bonded interactions (Kukol, Andreas) -- Message: 1 Date: Wed, 1 Jun 2011 15:32:07 -0400 From: Da-Wei Li lida...@gmail.com Subject: Re: [gmx-users] scaling non-bonded interactions To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTinww3_rE7x-SyffAPY=rwpyxt2...@mail.gmail.com Content-Type: text/plain; charset=utf-8 I remember that 1-4 won't be scaled in the free energy code, right? dawei On Wed, Jun 1, 2011 at 3:24 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kukol, Andreas wrote: Hello, Is it possible to globally scale all non-bonded interactions by a factor ? I know there are energy exclusion groups, but that is an all or nothing approach, while I would like to reduce non-bonded interaction potentials to e.g. 10% of their normal value. If this is not possible, I suggest to have this as an option in the mdp-file. You can do this with the free energy code. couple-moltype = system init_lambda = 0.9 couple_lambda0 = vdw-q couple_lambda1 = none Please note, though, that such settings will result in massive performance loss, even for small systems. There is an open issue on the redmine server about this, but no resolution yet. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110601/3f9a1391/attachment-0001.html -- Message: 2 Date: Wed, 1 Jun 2011 15:34:49 -0400 From: Miguel Quiliano Meza rifaxim...@gmail.com Subject: [gmx-users] question about trajcat command: Merge files To: gmx-users@gromacs.org Message-ID: BANLkTi=ai0nowvv_g3evvxxuqb1kcda...@mail.gmail.com Content-Type: text/plain
[gmx-users] Studying protein folding: An approach
Dear Community. I am a beginner user of Gromacs for this reason I would like to consult my case. Nowadays, I am studying a protein which folding process has experimental data (especially for a mutant). Structural information about how a mutant destabilizes secondary structure was recently published. The work shown how gradually increasing 1 C degree the structure is affected (from 18 to 20 C). I would like to study the process in silico, but I don´t know what parameters put in the .mdp file. Please their advices or help would be appreciated. Best Regards. Miguel Quiliano -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: How to install GROMACS in Rocks Cluster 5.4 : ERROR
Hi everyone. I followed the steps in http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites for my problem, but I obtained problems at the moment to perform make. So, as mention the web page of gromacs... If you get errors during GROMACS compilation (the make step) that suggest that you recompile with -fPIC, then you should return to this FFTW stage and configure with --enable-shared or --with-pic. By the way, previously I performed make with FFTW version 3.2.2 (default version in rocks cluster 5.4) I did: root@bioinfocluster fftw-3.2.2]# ./configure --enable-threads --prefix=/share/apps/opt/fftw Without errors, and then: [root@bioinfocluster fftw-3.2.2]# make make[3]: Leaving directory `/share/apps/src/fftw-3.2.2/tools' make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/tools' Making all in m4 make[2]: Entering directory `/share/apps/src/fftw-3.2.2/m4' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/share/apps/src/fftw-3.2.2/m4' make[1]: Leaving directory `/share/apps/src/fftw-3.2.2' What could be the problem? please advices. Miguel Quiliano. Miguel Quiliano Meza wrote: Dear community. Justin was right. I did not want to make the explanation so long, but you're right I have to put those details. As you will see I had to redirect the outputs after perform *./configure* and *make* (these files are attach to this mail). I sincerely hope you can give their opinions and help. Thanks in advance. Miguel Quiliano. Here are the general procedure: root@bioinfocluster src]# tar xf gromacs-4.5.4.tar.gz [root@bioinfocluster src]# export LDFLAGS=-L/opt/rocks/lib [root@bioinfocluster src]# export CPPFLAGS=-I/opt/rocks/include [root@bioinfocluster gromacs-4.5.4]# ./configure --enable-mpi --prefix=/share/apps/opt/gromacs output [root@bioinfocluster gromacs-4.5.4]# make output2 mempool.c: In function '_gmx_sel_mempool_alloc_group': mempool.c:201: warning: dereferencing type-punned pointer will break strict-aliasing rules selelem.c: In function '_gmx_selelem_mempool_reserve': selelem.c:203: warning: dereferencing type-punned pointer will break strict-aliasing rules selelem.c:208: warning: dereferencing type-punned pointer will break strict-aliasing rules checkpoint.c: In function 'do_cpt_state': checkpoint.c:852: warning: dereferencing type-punned pointer will break strict-aliasing rules /usr/bin/ld: /opt/rocks/lib/libfftw3f.a(plan-guru-dft-c2r.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC This issue and its resolution are specifically described in the installation instructions: http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites (Under the a few tips heading) -Justin /opt/rocks/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd_mpi.la http://libmd_mpi.la/] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all] Error 2 make: *** [all-recursive] Error 1 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR
Dear community. I have been trying to install gromacs 4.5.4 in my rocks cluster version 5.4 but unfortunately the system showed configure: error: Cannot find fftw3 library after launch the ./configure (you can see below) Really I do not understand because I did before this: # export LDFLAGS=-L/opt/rocks/lib # export CPPFLAGS=-I/opt/rocks/include # ./configure --enable-mpi --disable-float --prefix=/share/apps/opt/gromacs configure: error: Cannot find fftw3 library I would be very grateful if someone could help me or give me advices. By the way... I am trying to reproduce the steps posted in http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/for compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0 and the option --disable-float is not clear for me. Thank you in advance. Miguel Quiliano. P.S I attach the error # ./configure --enable-mpi --disable-float --prefix=/share/apps/opt/gromacs checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for MPI_IN_PLACE in collective operations... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether mpicc accepts -O3... yes checking whether mpicc accepts -msse2... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -std=gnu99... yes checking whether mpicc accepts -fexcess-precision=fast... no checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by mpicc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... yes checking whether mpicc accepts -g... yes checking dependency style of mpicc... gcc3 checking how to run the C++ preprocessor... mpicc -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from mpicc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC checking if mpicc PIC flag -fPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes configure: creating libtool appending configuration tag CXX to libtool checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld
[gmx-users] Re: gmx-users Digest, Vol 84, Issue 90
comm_grps = System to avoid possible instability. If you're interested in diffusion-related properties, on the other hand, that may not be appropriate. Plenty to think about, but again, probably no easy solution. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 2 Date: Mon, 11 Apr 2011 14:01:58 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] How to install GROMACS in Rocks Cluster 4.5.4 : ERROR To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4da34216.9050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Miguel Quiliano Meza wrote: Dear community. I have been trying to install gromacs 4.5.4 in my rocks cluster version 5.4 but unfortunately the system showed configure: error: Cannot find fftw3 library after launch the ./configure (you can see below) Really I do not understand because I did before this: # export LDFLAGS=-L/opt/rocks/lib # export CPPFLAGS=-I/opt/rocks/include # ./configure --enable-mpi --disable-float --prefix=/share/apps/opt/gromacs configure: error: Cannot find fftw3 library You have a precision mismatch. By using --disable-float you are trying to install Gromacs in double precision (which for most applications is not necessary and results in some performance loss). Thus, you need FFTW in double precision as well. You probably compiled FFTW in single precision, thus the libraries are named libfftw3f, not libfftw3. -Justin I would be very grateful if someone could help me or give me advices. By the way... I am trying to reproduce the steps posted in http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/ for compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0 and the option --disable-float is not clear for me. Thank you in advance. Miguel Quiliano. P.S I attach the error # ./configure --enable-mpi --disable-float --prefix=/share/apps/opt/gromacs checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for MPI_IN_PLACE in collective operations... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether mpicc accepts -O3... yes checking whether mpicc accepts -msse2... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -std=gnu99... yes checking whether mpicc accepts -fexcess-precision=fast... no checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking whether byte ordering is bigendian... no checking that size_t can
[gmx-users] how to Installing GROMACS in rocks cluster
Dear Colleagues. I have been searching information about HOW TO INSTALL GROMACS in rocks cluster?. Unfortunately, the information that I found is not clear. Someone can help me with this question. Maybe there are basic but important steps that I have to keep in mind. Could you please share yours experiences? Thank you in advance. Miguel Quiliano. P.D I have installed rocks cluster 5.4 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 84, Issue 28
Dear colleagues. I would like to share with the community this. Searching I can find this: http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/ Compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0I think is very useful for People who have the same objective. However, in one section the tutorial refers that the GROMACS version 4.5.3 had some bugs. I would like to install version GROMACS 4.5.4, Does somebody know if this version has the same problems? Thanks in advance. Miguel Quiliano. 2011/4/4 gmx-users-requ...@gromacs.org Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. how to Installing GROMACS in rocks cluster (Miguel Quiliano Meza) 2. autocorrelation functions (shivangi nangia) 3. Re: FEP and loss of performance (Luca Bellucci) 4. g_chi (simon sham) 5. Re: g_chi (Francesco Oteri) 6. Re: g_chi (Justin A. Lemkul) -- Message: 1 Date: Mon, 4 Apr 2011 13:58:40 -0400 From: Miguel Quiliano Meza rifaxim...@gmail.com Subject: [gmx-users] how to Installing GROMACS in rocks cluster To: gmx-users@gromacs.org Message-ID: BANLkTimh_Lx_E9B=fJ-WRypK-vh=cf2...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear Colleagues. I have been searching information about HOW TO INSTALL GROMACS in rocks cluster?. Unfortunately, the information that I found is not clear. Someone can help me with this question. Maybe there are basic but important steps that I have to keep in mind. Could you please share yours experiences? Thank you in advance. Miguel Quiliano. P.D I have installed rocks cluster 5.4 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110404/ef4b39fe/attachment-0001.html -- Message: 2 Date: Mon, 4 Apr 2011 14:11:48 -0400 From: shivangi nangia shivangi.nan...@gmail.com Subject: [gmx-users] autocorrelation functions To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTi=HS9T7zpWkhEVFsYmZjrV=he1...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to modify/morph the g_velacc.c program to do other autocorrelation function calculations? Thanks, Shivangi -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110404/cb2a4e0a/attachment-0001.html -- Message: 3 Date: Mon, 4 Apr 2011 20:36:37 +0200 From: Luca Bellucci lcbl...@gmail.com Subject: Re: [gmx-users] FEP and loss of performance To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 201104042036.37450.lcbl...@gmail.com Content-Type: text/plain; charset=utf-8 Yes i am testing the possibility to perform an Hamiltonian-REMD Energy barriers can be overcome increasing the temperature system or scaling potential energy with a lambda value, these methods are equivalent. Both have advantages and disavantages, at this stage it is not the right place to debate on it. The main problem seems to be how to overcome to the the loss of gromacs performance in such calculation. At this moment it seems an intrinsic code problem. Is it possible? Dear Chris and Justin / Thank you for your precious suggestions // This is a test that i perform in a single machine with 8 cores // and gromacs 4.5.4. // // I am trying to enhance the sampling of a protein using the decoupling scheme // of the free energy module of gromacs. However when i decouple only the // protein, the protein collapsed. Because i simulated in NVT i thought that // this was an effect of the solvent. I was trying to decouple also the solvent // to understand the system behavior. // / Rather than suspect that the solvent is the problem, it's more likely that decoupling an entire protein simply isn't stable. I have never tried anything that enormous, but the volume change in the system could be unstable, along with any number of factors, depending on how you approach
[gmx-users] Fe+2 not found in forcefield ffG43a1
Dear Users. Maybe this question is easy for all, but i have problems, patience please. I do not have experience with metals, now I have a protein (crystal) with Fe+2, which is coordinating with three HISTIDINES, one D and two molecules of water, when I try to run pdb2gmx the program tells me Residue FE not found in residue topology database. I opened the database for forcefield ffG43a1 and only found FE for heme group. I search other forcefields for iron+2, but most refer to heme groups. Why? and what happend with Fe+2? What can i do? I would very grateful if someone gives advices or ideas. thanks in advance Miguel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] an energy minimization question, working with H-BONDS
Dear Users. I am a relative new user of GROMACS and I have some doubts: I would like to perform a energy minimization (with water and iones) of a crystal in orden to re-build the H-bonds responsible of the secundary structure, to achieve this goal I want to restraint the movement of the protein (aminoacids) and permit the movement of the H-bonds as a product of add Hydrogens with pdb2gmx. I think that this task could be define/establish in CONSTRAINS in the .mdp file, I searched in the web and only find this: Bonds constraints: *none* No constraints except for those defined explicitly in the topology, i.e. bonds are represented by a harmonic (or other) potential or a Morse potential (depending on the setting of *morse*) and angles by a harmonic (or other) potential. *hbonds* Convert the bonds with H-atoms to constraints. *all-bonds* Convert all bonds to constraints. * h-angles* Convert all bonds and additionally the angles that involve H-atoms to bond-constraints. *all-angles* Convert all bonds and angles to bond-constraints. What option shoud I use for my objective? My objetive, is it possible to do? I would be very grateful if someone can help me with some ideas or advices. thanks in advance Miguel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the solvent group SOL is not continuous
*Hi everyone. I have a problem when I try to run GENION, GROMACS says: * WARNING: turning of free energy, will use lambda=0 Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision) Using a coulomb cut-off of 0.9 nm Will try to add 0 Na ions and 15 NA+ ions. Select a continuous group of solvent molecules Opening library file /usr/share/gromacs/top/ aminoacids.dat Group 0 ( System) has 275439 elements Group 1 ( Protein) has 1722 elements Group 2 ( Protein-H) has 1371 elements Group 3 ( C-alpha) has 185 elements Group 4 (Backbone) has 555 elements Group 5 ( MainChain) has 741 elements Group 6 (MainChain+Cb) has 909 elements Group 7 ( MainChain+H) has 921 elements Group 8 ( SideChain) has 801 elements Group 9 ( SideChain-H) has 630 elements Group10 ( Prot-Masses) has 1722 elements Group11 ( Non-Protein) has 273717 elements Group12 ( ZN) has 1 elements Group13 ( SOL) has 273702 elements Group14 ( LIG) has14 elements Group15 ( Other) has 273717 elements Select a group: 13 Selected 13: 'SOL' --- Program genion, VERSION 3.3.3 Source code file: ../../../../src/tools/gmx_genion.c, line: 429 Fatal error: The solvent group SOL is not continuous: index[9]=1732, index[10]=1747 --- Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is. (Jackie Brown) *I do not know the reason,the number of residues in top file and pdb file are the same. The only warning that I saw was when I ran grompp: * WARNING 1 [file 1x8a.top, line unknown]: The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2 NH, OH, CO2, CO, etc. *Coincidentally they are some of the atomos of my ligand* * I have been reading the web and no-one says nothing about it. I would be very grateful if someone can help me or give me advices. Best Regards MIguel Quiliano* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 69, Issue 133
Hi , Justin. well.. I keep three water molecules from original PDB , my actual model was obtained by homology. my file *top shows this. [ molecules ] ; Compound#mols Protein 1 -- Also, Zn+2 is here SOL 3 from template LIG 1 SOL 91231---added with genbox Now, in my *pdb file obtained with genbox there are no blocks, ... ... ATOM 1721 O1 SER 185 78.315 86.779 66.412 1.00 0.00 ATOM 1722 O2 SER 185 78.467 89.180 66.704 1.00 0.00 ATOM 1723 Zn ZN 186 70.487 59.483 68.899 1.00 0.00 ATOM 1724 OW HOH 187 69.331 58.199 67.904 1.00 0.00 ATOM 1725 HW1 HOH 187 70.147 58.199 68.481 1.00 0.00 ATOM 1726 HW2 HOH 187 68.515 58.199 68.481 1.00 0.00 ATOM 1727 OW HOH 188 70.810 60.669 67.316 1.00 0.00 ATOM 1728 HW1 HOH 188 71.626 60.669 67.893 1.00 0.00 ATOM 1729 HW2 HOH 188 70.810 61.485 66.739 1.00 0.00 ATOM 1730 OW HOH 189 68.765 60.471 69.225 1.00 0.00 ATOM 1731 HW1 HOH 189 69.581 60.471 69.802 1.00 0.00 ATOM 1732 HW2 HOH 189 68.765 59.655 68.648 1.00 0.00 ATOM 1733 CAB LIG 190 71.884 63.353 62.792 1.00 0.00 ATOM 1734 HAB LIG 190 70.812 63.372 62.596 1.00 0.00 .. ATOM 1746 HAI LIG 190 72.792 64.517 66.353 1.00 0.00 ATOM 1747 OW SOL 191 5.690 12.751 11.651 1.00 0.00 ATOM 1748 HW1 SOL 191 4.760 12.681 11.281 1.00 0.00 ATOM 1749 HW2 SOL 191 5.800 13.641 12.091 1.00 0.00 ATOM 1750 OW SOL 192 15.551 15.111 7.030 1.00 0.00 ATOM 1751 HW1 SOL 192 14.981 14.951 7.840 1.00 0.00 . .. What could be the problem?? thanks in advance. MIguel. 2010/1/26 gmx-users-requ...@gromacs.org Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: the solvent group SOL is not continuous (Justin A. Lemkul) 2. Potential Energy (Yanmei Song) 3. RE?: gmx-users Digest, Vol 69, Issue 132 (ABEL Stephane 175950) -- Message: 1 Date: Tue, 26 Jan 2010 16:30:07 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] the solvent group SOL is not continuous To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b5f5edf.4080...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Miguel Quiliano Meza wrote: *Hi everyone. I have a problem when I try to run GENION, GROMACS says: * WARNING: turning of free energy, will use lambda=0 Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision) Using a coulomb cut-off of 0.9 nm Will try to add 0 Na ions and 15 NA+ ions. Select a continuous group of solvent molecules Opening library file /usr/share/gromacs/top/ aminoacids.dat Group 0 ( System) has 275439 elements Group 1 ( Protein) has 1722 elements Group 2 ( Protein-H) has 1371 elements Group 3 ( C-alpha) has 185 elements Group 4 (Backbone) has 555 elements Group 5 ( MainChain) has 741 elements Group 6 (MainChain+Cb) has 909 elements Group 7 ( MainChain+H) has 921 elements Group 8 ( SideChain) has 801 elements Group 9 ( SideChain-H) has 630 elements Group10 ( Prot-Masses) has 1722 elements Group11 ( Non-Protein) has 273717 elements Group12 ( ZN) has 1 elements Group13 ( SOL) has 273702 elements Group14 ( LIG) has14 elements Group15 ( Other) has 273717 elements Select a group: 13 Selected 13: 'SOL' --- Program genion, VERSION 3.3.3 Source code file: ../../../../src/tools/gmx_genion.c, line: 429 Fatal error: The solvent group SOL is not continuous: index[9]=1732, index[10]=1747 --- Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is. (Jackie Brown) *I do not know the reason,the number of residues in top file and pdb file are the same. The only warning that I saw was when I ran grompp: * WARNING 1 [file 1x8a.top, line unknown]: The largest charge group contains 11 atoms. Since atoms only see each other when the centers
[gmx-users] checkpoint MDRUN -cpt question
Hi everyone. I am a relative new user of GROMACS. I have performed some short simulations but now I want to something big. I have been reading on the web site and found that mdrun -.cpt option is used to generate checkpoints, I am using GROMACS 3.3.3 but I don't find -cpt option when I call mdrun -h I would very grateful if someone can help me with how to do a checkpoint with GROMACS 3.3.3? Best Regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to save information even after stopping calculation
Dear gromacs users I am running a molecular dynamics calculation, all is fine but the time of calculation is big, I would like to know if I can stop the calculation without lose the information generated until that point. thanks in advance. Miguel Quiliano. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] help with FAD topology, please
Dear all. I am a new user of GROMACS, I have read the user book and free tutorials in the WEB, but now when I try to do a simulation, appears FAD no topology, I have been reading that PRODRG server is a way to achieve that goal, I tried but the output format is different, it means old version (for gromos 96 forcefield). I do not mind edit by hand (I want to learn), I searched in the gmx-users but no one shares the FAD topology. Until now, I can't run my simulation. So, I would be very grateful if someone could give me tips, advices or the FAD topology (in this way I could see my errors). Thanks in advance. Miguel. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
