[gmx-users] Re: about gromacs-osx-intel-3.3.1.dmg
Dear Users, actually, libXm.2.dylib is missing. Could anyboby tell me how to get this file? Thanks >liang wrote: >> Dear Users, >> >> i would like to install gromacs on Mac OSX tiger 10.4.10, and i download >> this dmg file from ftp site. >> after i installed successfully, i tried to test some commands >> but it showed some warnings: >> >> dyld: Library not loaded: /usr/local/gromacs/lib/libmd.4.dylib >does this library exist? Or did you put it in another directory? >>Referenced from: /Users/Wayne/Gromacs/bin/mdrun >>Reason: image not found >> Trace/BPT trap >> >> it seems to lack a lib file, but i dont know how to get it. >> does anyone give me some advice? >> >> Thanks so much !!! ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: about gromacs-osx-intel-3.3.1.dmg
liang wrote: > Dear Users, > > actually, libXm.2.dylib is missing. You may want to install fink and the finkcommander, which provides you with a graphical user interface for installing free software packages (including gromacs...). Anyway, once you have that you need to install openmotif. > > Could anyboby tell me how to get this file? > > Thanks > > >liang wrote: > >> Dear Users, > >> > >> i would like to install gromacs on Mac OSX tiger 10.4.10, and i > download > >> this dmg file from ftp site. > >> after i installed successfully, i tried to test some commands > >> but it showed some warnings: > >> > >> dyld: Library not loaded: /usr/local/gromacs/lib/libmd.4.dylib > > >does this library exist? Or did you put it in another directory? > > >>Referenced from: /Users/Wayne/Gromacs/bin/mdrun > >>Reason: image not found > >> Trace/BPT trap > >> > >> it seems to lack a lib file, but i dont know how to get it. > >> does anyone give me some advice? > >> > >> Thanks so much !!! > > > > > ___ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: about gromacs-osx-intel-3.3.1.dmg
liang wrote: > Dear Users, > > actually, libXm.2.dylib is missing. > > Could anyboby tell me how to get this file? This belongs to Motif or Lesstif libraries. Of all the gromacs tools, only ngmx requires it, and since it's a very optional tool, you can turn off building it with a configure option. Check "./configure --help" for the details. Alternatively, you can presumably install Lesstif for Mac readily. Mark ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] hi
I want to perform simulation of transmembrane peptide. I have a perseuillibrated POPO (hydrated) bilayer (using CHARMM),containing more than 32,000 atom. But when I try to convert ".pdb" to ".gro" using "pdb2gmx", it shows the following error Fatal error: Residue "popc" not found in residue topology detabase Please suggest how I can overcome this problem . Moutusi 5, 50, 500, 5000 - Store N number of mails in your inbox. Go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] hi
Moutusi Manna wrote: I want to perform simulation of transmembrane peptide. I have a perseuillibrated POPO (hydrated) bilayer (using CHARMM),containing more than 32,000 atom. But when I try to convert ".pdb" to ".gro" using "pdb2gmx", it shows the following error The role of pdb2gmx is not convert a .pdb to a .gro, it is to generate a topology file from a structure file. It outputs a structure file that is consistent with that topology file, but that structure file can be in several formats. See pdb2gmx -h. Fatal error: Residue "popc" not found in residue topology detabase Please suggest how I can overcome this problem . http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database If this makes no sense (and even if it does) reading relevant parts of chapter 5 of the GROMACS manual will be needed here. Mark ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem during converting ".pdb" to ".gro"
I want to perform simulation of trans-membrane peptide. I have a equilibrated POPC (hydrated) bilayer (using CHARMM),containing more than 32,000 atom. But when I try to convert ".pdb" to ".gro" using "pdb2gmx", it shows the following error Fatal error: Residue "popc" not found in residue topology database Please suggest how I can overcome this problem . Get the freedom to save as many mails as you wish. To know how, go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem during converting ".pdb" to ".gro"
Moutusi Manna wrote: I want to perform simulation of trans-membrane peptide. I have a equilibrated POPC (hydrated) bilayer (using CHARMM),containing more than 32,000 atom. But when I try to convert ".pdb" to ".gro" using "pdb2gmx", it shows the following error Fatal error: Residue "popc" not found in residue topology database Please suggest how I can overcome this problem . http://wiki.gromacs.org Get the freedom to save as many mails as you wish. To know how, go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to Install GMX V3.3.1 with Intel fortran compiler?
Dear GMX-users: I've searched the list but couldnt find something usful for me, and this is how I did it so far : source /opt/intel/fce/version/bin/ifortvars.sh export F77=ifort export CPPFLAGS=-I/home/xin/programs/fftw312/include export LDFLAGS=-L/home/dong/programs/fftw312/lib configure --prefix=/home/xin/programs/gromacs331 --enable-fortran --enable-mpi make mdrun make install-mdrun after the installation, I tried to do the mdrun: mpirun -np 2 /home/xin/programs/gromacs331/mdrun -s ... and then I got the following error message: error while loading shared libraries: libsvml.so: cannot open shared object file: No such file or directory The OS of my pc is SUSE 9.3. And I found that the "missing" file, libsvml.so, was in /opt/intel/fce/version/lib Is there something wrong with my steps? or shoould I add some FFLAGS? I am not very familiar with fortran and Linux, any suggestions will be appreciated! Xin Liu ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installation problem on gromacs 3.3.1 during the step make install
You get plenty of "these are the same file" error look: /people/mail/mariag/gromacs-3.3.1/man/man1/anadock.1' are the same file try to make install to a different folder than the one you extracted the source (.tgz) PWD = /people/mail/mariag/ %tar xvfz gromacs-3.3.1.tgz %cd /people/mail/mariag/gromacs-3.3.1/ %make distclean %./configure --prefix=/people/mail/mariag/gmx331/ %make %make install On 9/11/07, maria goranovic <[EMAIL PROTECTED]> wrote: > > Hi, > > I am trying to install a serial version of 3.3.1 on my suse 10.2 linux > box. I am attempting this installation on my home directory, and do not have > root access. > > I think I have followed all the steps exactly and get an error while doing > the final make install. The final part of the log file is attached below. > > PS1: I do use make distclean before each new attempt at ./configure > PS2: my home directory is /people/mail/mariag > > Help, please ? > > Thank you very much, > > -Maria > > > > > Making install in man1 > make[2]: Entering directory `/people/mail/mariag/gromacs-3.3.1/man/man1' > make[3]: Entering directory `/people/mail/mariag/gromacs-3.3.1/man/man1' > make[3]: Nothing to be done for `install-exec-am'. > test -z "/people/mail/mariag/gromacs-3.3.1/man/man1" || mkdir -p -- > "/people/mail/mariag/gromacs-3.3.1/man/man1" > /usr/bin/install -c -m 644 './anadock.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/anadock.1' > /usr/bin/install: `./anadock.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/anadock.1' > are the same file > /usr/bin/install -c -m 644 './g_cluster.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/g_cluster.1' > /usr/bin/install: `./g_cluster.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/g_cluster.1' > are the same file > /usr/bin/install -c -m 644 './g_filter.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/g_filter.1' > /usr/bin/install: `./g_filter.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/g_filter.1' > are the same file > /usr/bin/install -c -m 644 './g_potential.1' > '/people/mail/mariag/gromacs- 3.3.1/man/man1/g_potential.1' > /usr/bin/install: `./g_potential.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/g_potential.1' > are the same file > /usr/bin/install -c -m 644 './g_velacc.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/g_velacc.1' > /usr/bin/install: `./g_velacc.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/g_velacc.1' > are the same file > /usr/bin/install -c -m 644 './ngmx.1' '/people/mail/mariag/gromacs- 3.3.1 > /man/man1/ngmx.1' > /usr/bin/install: `./ngmx.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/ngmx.1' > are the same file > /usr/bin/install -c -m 644 './cdist.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/cdist.1' > /usr/bin/install: `./cdist.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/cdist.1' > are the same file > /usr/bin/install -c -m 644 './g_clustsize.1' > '/people/mail/mariag/gromacs- 3.3.1/man/man1/g_clustsize.1' > /usr/bin/install: `./g_clustsize.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/g_clustsize.1' > are the same file > /usr/bin/install -c -m 644 './g_gyrate.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/g_gyrate.1' > /usr/bin/install: `./g_gyrate.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/g_gyrate.1' > are the same file > /usr/bin/install -c -m 644 './g_rama.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/g_rama.1' > /usr/bin/install: `./g_rama.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/g_rama.1' > are the same file > /usr/bin/install -c -m 644 './g_wham.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/g_wham.1' > /usr/bin/install: `./g_wham.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/g_wham.1' > are the same file > /usr/bin/install -c -m 644 './pdb2gmx.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/pdb2gmx.1' > /usr/bin/install: `./pdb2gmx.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/pdb2gmx.1' > are the same file > /usr/bin/install -c -m 644 './disco.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/disco.1' > /usr/bin/install: `./disco.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/disco.1' > are the same file > /usr/bin/install -c -m 644 './g_confrms.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/g_confrms.1' > /usr/bin/install: `./g_confrms.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/g_confrms.1' > are the same file > /usr/bin/install -c -m 644 './g_h2order.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/g_h2order.1' > /usr/bin/install: `./g_h2order.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/g_h2order.1' > are the same file > /usr/bin/install -c -m 644 './g_rdf.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/g_rdf.1' > /usr/bin/install: `./g_rdf.1' and > `/people/mail/mariag/gromacs-3.3.1/man/man1/g_rdf.1' > are the same file > /usr/bin/install -c -m 644 './genbox.1' '/people/mail/mariag/gromacs- > 3.3.1/man/man1/genbox.1' > /usr/bin/install:
Re: [gmx-users] How to Install GMX V3.3.1 with Intel fortran compiler?
This works for me: % vim /etc/ld.conf /opt/intel/mkl/8.0/lib/em64t/ <<<= only if you have installed MKL /opt/intel/fce/9.0/lib/ /opt/intel/cce/9.0/lib/ then run % ldconfig If you wish, you may also add the 32bit libs: /opt/intel/mkl/8.0/lib/32/ <<<= only if you have installed MKL /opt/intel/fc/9.0/lib/ /opt/intel/cc/9.0/lib/ On 9/13/07, liu xin <[EMAIL PROTECTED]> wrote: > > Dear GMX-users: > > I've searched the list but couldnt find something usful for me, and this > is how I did it so far : > > source /opt/intel/fce/version/bin/ifortvars.sh > export F77=ifort > export CPPFLAGS=-I/home/xin/programs/fftw312/include > export LDFLAGS=-L/home/dong/programs/fftw312/lib > configure --prefix=/home/xin/programs/gromacs331 --enable-fortran > --enable-mpi > make mdrun > make install-mdrun > > after the installation, I tried to do the mdrun: > mpirun -np 2 /home/xin/programs/gromacs331/mdrun -s ... > and then I got the following error message: > error while loading shared libraries: libsvml.so: cannot open shared > object file: No such file or directory > > The OS of my pc is SUSE 9.3. And I found that the "missing" file, > libsvml.so, was in /opt/intel/fce/version/lib > Is there something wrong with my steps? or shoould I add some FFLAGS? > I am not very familiar with fortran and Linux, any suggestions will be > appreciated! > > Xin Liu > > ___ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to Install GMX V3.3.1 with Intel fortran compiler?
Hi, Well, I have a much simpler solution - there is no reason whatsoever to use fortran on ia32 or x86-64 since Gromacs will always use the much faster SSE assembly loops. Cheers, Erik On Sep 13, 2007, at 8:44 AM, Diego Enry wrote: This works for me: % vim /etc/ld.conf /opt/intel/mkl/8.0/lib/em64t/ <<<= only if you have installed MKL /opt/intel/fce/9.0/lib/ /opt/intel/cce/9.0/lib/ then run % ldconfig If you wish, you may also add the 32bit libs: /opt/intel/mkl/8.0/lib/32/ <<<= only if you have installed MKL /opt/intel/fc/9.0/lib/ /opt/intel/cc/9.0/lib/ On 9/13/07, liu xin <[EMAIL PROTECTED]> wrote: Dear GMX-users: I've searched the list but couldnt find something usful for me, and this is how I did it so far : source /opt/intel/fce/version/bin/ifortvars.sh export F77=ifort export CPPFLAGS=-I/home/xin/programs/fftw312/include export LDFLAGS=-L/home/dong/programs/fftw312/lib configure --prefix=/home/xin/programs/gromacs331 --enable-fortran -- enable-mpi make mdrun make install-mdrun after the installation, I tried to do the mdrun: mpirun -np 2 /home/xin/programs/gromacs331/mdrun -s ... and then I got the following error message: error while loading shared libraries: libsvml.so: cannot open shared object file: No such file or directory The OS of my pc is SUSE 9.3. And I found that the "missing" file, libsvml.so, was in /opt/intel/fce/version/lib Is there something wrong with my steps? or shoould I add some FFLAGS? I am not very familiar with fortran and Linux, any suggestions will be appreciated! Xin Liu ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to Install GMX V3.3.1 with Intel fortran compiler?
Hi. Yes, but that is the "gcc solution". No prblem with those, except for giving away the "challenge" to make it work with intel compilers. Basically: I couldn't find a way much better. The way I trid in the time I tried, included compilation of the loops and only the loops using gcc to make the assembly works... :P Sad, the computer won that on me... :P Wish you have better luck! :) Jones On 9/13/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: > > Hi, > Well, I have a much simpler solution - there is no reason whatsoever to > use fortran on ia32 or x86-64 since Gromacs will always use the much faster > SSE assembly loops. > > Cheers, > > Erik > > > On Sep 13, 2007, at 8:44 AM, Diego Enry wrote: > > This works for me: > > % vim /etc/ld.conf > > /opt/intel/mkl/8.0/lib/em64t/ <<<= only if you have installed > MKL > /opt/intel/fce/9.0/lib/ > /opt/intel/cce/9.0/lib/ > > then run > % ldconfig > > > If you wish, you may also add the 32bit libs: > /opt/intel/mkl/8.0/lib/32/ <<<= only if you have installed MKL > /opt/intel/fc/9.0/lib/ > /opt/intel/cc/9.0/lib/ > > > > On 9/13/07, liu xin <[EMAIL PROTECTED]> wrote: > > > > Dear GMX-users: > > > > I've searched the list but couldnt find something usful for me, and this > > is how I did it so far : > > > > source /opt/intel/fce/version/bin/ifortvars.sh > > export F77=ifort > > export CPPFLAGS=-I/home/xin/programs/fftw312/include > > export LDFLAGS=-L/home/dong/programs/fftw312/lib > > configure --prefix=/home/xin/programs/gromacs331 --enable-fortran > > --enable-mpi > > make mdrun > > make install-mdrun > > > > after the installation, I tried to do the mdrun: > > mpirun -np 2 /home/xin/programs/gromacs331/mdrun -s ... > > and then I got the following error message: > > error while loading shared libraries: libsvml.so: cannot open shared > > object file: No such file or directory > > > > The OS of my pc is SUSE 9.3. And I found that the "missing" file, > > libsvml.so, was in /opt/intel/fce/version/lib > > Is there something wrong with my steps? or shoould I add some FFLAGS? > > I am not very familiar with fortran and Linux, any suggestions will be > > appreciated! > > > > Xin Liu > > > > ___ > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Diego Enry B. Gomes > Laboratório de Modelagem e Dinamica Molecular > Universidade Federal do Rio de Janeiro - Brasil. > ___ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ___ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Applying a Uniform Shear
Hello, I am looking for a way in Gromacs that I could apply a uniform shear. I have looked through the manual, and it seems that the methods for applying shear are using the cos_acceleration option or the deform option. The deform option may work for me. However, I was reading in Allen and Tildesley's book about a method for applying a uniform shear which involves a modification to the PBC (In fact, I think it is what's depicted on the book's cover). Essentially, the simulation box is held fixed, and the boxes above move in one direction (+x) and the boxes below move in the opposite direction (-x). Is there any way that I can do something like this in Gromacs? I have searched the mailing list as well, but have come up empty handed. My system is a lipid bilayer in water. I would like to look at this system's response to a shear force, but I am not interested in any viscosity calculations, so I am not sure cos_acceleration would be helpful to me. If I use deform, I am worried that at long times I will get a simulation box with some very sharp angles. If the above procedure is not possible in Gromacs, would it make sense to use the deform option in a sinusoidal fashion doing several simulations where the box is first deformed one way and then deformed back again in the opposite direction? Thank you, Mike ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Applying a Uniform Shear
toma0052 wrote: Hello, I am looking for a way in Gromacs that I could apply a uniform shear. I have looked through the manual, and it seems that the methods for applying shear are using the cos_acceleration option or the deform option. The deform option may work for me. However, I was reading in Allen and Tildesley's book about a method for applying a uniform shear which involves a modification to the PBC (In fact, I think it is what's depicted on the book's cover). Essentially, the simulation box is held fixed, and the boxes above move in one direction (+x) and the boxes below move in the opposite direction (-x). Is there any way that I can do something like this in Gromacs? I have searched the mailing list as well, but have come up empty handed. My system is a lipid bilayer in water. I would like to look at this system's response to a shear force, but I am not interested in any viscosity calculations, so I am not sure cos_acceleration would be helpful to me. If I use deform, I am worried that at long times I will get a simulation box with some very sharp angles. If the above procedure is not possible in Gromacs, would it make sense to use the deform option in a sinusoidal fashion doing several simulations where the box is first deformed one way and then deformed back again in the opposite direction? you can use normal accelerations (see mdp options) Thank you, Mike ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] genbox & protein internal H2O
Hi, I am wanting to solvate a protein w/o adding H2O to its interior. Reasons: 1. I am interested to know how the structural H2Os behave initially w/o interference from added H2O. 2. Added H2O also introduce steric constraints that prevent EM from achieving its goal, even w/o constraints. Have there been additional ideas since the following suggestions were made: http://wiki.gromacs.org/index.php/genbox I have no trouble identifying interior structural H2Os before solvation. After solvation the visual field is cluttered w/ added H2O and is harder to work with. Ideally I'd like to hide all added H2O outside the solvent accessible surface or perhaps a little farther out, and then work w/ molecular visualization. Suggestions would be welcome? A second question is that if I identify added interior H2Os and remove them, there will be spots in files that are not sequentially numbered. Do gromacs programs care about this? -John ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Applying a Uniform Shear
Hello, Thanks for the rapid response, although I am not sure I completely understand what you mean. The accelerate option adds a constant acceleration to whatever atoms I choose with acc_grps. However, if I want a uniform shear, I need to give atoms an acceleration dependent on their position within the simulation box (z-coordinate in the case of my bilayer lying in the x-y plane and the acceleration being in the x-direction). I don't see how I could do this with the accelerate mdp option. Am I missing something here? Thanks, Mike On 13 Sep 2007, David van der Spoel wrote: > toma0052 wrote: > > Hello, > > I am looking for a way in Gromacs that I could apply a uniform shear. > I > > have looked through the manual, and it seems that the methods for applying > > shear are using the cos_acceleration option or the deform option. The > deform > > option may work for me. However, I was reading in Allen and Tildesley's > book > > about a method for applying a uniform shear which involves a modification > to > > the PBC (In fact, I think it is what's depicted on the book's cover). > > Essentially, the simulation box is held fixed, and the boxes above move in > > one direction (+x) and the boxes below move in the opposite direction (-x). > > > Is there any way that I can do something like this in Gromacs? I have > > searched the mailing list as well, but have come up empty handed. > > My system is a lipid bilayer in water. I would like to look at this > > system's response to a shear force, but I am not interested in any > viscosity > > calculations, so I am not sure cos_acceleration would be helpful to me. If > I > > use deform, I am worried that at long times I will get a simulation box > with > > some very sharp angles. If the above procedure is not possible in Gromacs, > > would it make sense to use the deform option in a sinusoidal fashion doing > > several simulations where the box is first deformed one way and then > deformed > > back again in the opposite direction? > > > > > you can use normal accelerations (see mdp options) > > > Thank you, > > Mike > > > > ___ > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Applying a Uniform Shear
toma0052 wrote: Hello, Thanks for the rapid response, although I am not sure I completely understand what you mean. The accelerate option adds a constant acceleration to whatever atoms I choose with acc_grps. However, if I want a uniform shear, I need to give atoms an acceleration dependent on their position within the simulation box (z-coordinate in the case of my bilayer lying in the x-y plane and the acceleration being in the x-direction). I don't see how I could do this with the accelerate mdp option. Am I missing something here? I see. In that case you'll have to do a tiny bit of programming. Check src/mdlib/update.c Thanks, Mike On 13 Sep 2007, David van der Spoel wrote: toma0052 wrote: Hello, I am looking for a way in Gromacs that I could apply a uniform shear. I have looked through the manual, and it seems that the methods for applying shear are using the cos_acceleration option or the deform option. The deform option may work for me. However, I was reading in Allen and Tildesley's book about a method for applying a uniform shear which involves a modification to the PBC (In fact, I think it is what's depicted on the book's cover). Essentially, the simulation box is held fixed, and the boxes above move in one direction (+x) and the boxes below move in the opposite direction (-x). Is there any way that I can do something like this in Gromacs? I have searched the mailing list as well, but have come up empty handed. My system is a lipid bilayer in water. I would like to look at this system's response to a shear force, but I am not interested in any viscosity calculations, so I am not sure cos_acceleration would be helpful to me. If I use deform, I am worried that at long times I will get a simulation box with some very sharp angles. If the above procedure is not possible in Gromacs, would it make sense to use the deform option in a sinusoidal fashion doing several simulations where the box is first deformed one way and then deformed back again in the opposite direction? you can use normal accelerations (see mdp options) Thank you, Mike ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] calculation the energy of interaction
Hello everybody,
I have a system made of lipid and water and I want to calculate the
components of the lipid-lipid, lipid-water and water solvent
interactions (LJ+electrostatics). I know there is already a lot of
explanations about that kind of stuff on the mailing-list. I have
carefully read all of them. Probably too carefully because I'm pretty
confused now :(. Can someone tell me if my protocol is correct or not?
0. As a preliminary remark, I may need to specify my MD parameters:
vdwtype = Cut-off
rvdw = 1.4
coulombtype = PME
rcoulomd = 1.0
rlist=1.0
1. For the LJ interactions:
There is not much to do except running g_energy. For the Lipid-Water LJ
interactions, I just have to sum LJ-SR:DOPC-SOL + LJ-LR:DOPC-SOL. Same
thing for Lipid-Lipid and Water-Water interactions
2. For the Electrostatic interactions:
Still with g_energy, I can get the Coul-SR interactions. But Coul-LR
need additional calculations because of the PME. I need to rerun my
trajectory with
- a. charge set to 0.00 on water molecules
- b. charge set to 0.00 on POPC molecules
Then, the Coul-LR:DOPC-DOPC term is equal to the Coul.-recip. in run 'a'
and the Coul-LR:SOL-SOL term is equal to the Coul.-recip. in run 'b'.
The Coul-LR:DOPC-SOL is equal to the Coul.-recip. of the initial run.
Now, I just have to sum Coul-SR and Coul-LR
3. Now, what if I want to measure the head group-water interactions
(supposing the group is correctly defined in my .ndx)? For the LJ and
the short range electrostatic interactions, it is the same thing than
previously. For the long range electrostatic interactions, I need to do
more rerun with :
- c. charge set to 0.00 on everything except lipid head groups
- d. charge set to 0.00 on everything except water molecules
- e. charge set to 0.00 on everything except head groups and water
- f. charge set to 0.00 on everything except acyl chains and water
- g. charge set to 0.00 on everything except acyl chains and head groups
- h. charge set to 0.00 on everything except acyl chains
Then, Coul-LR:headgroup-headgroup=Coul.-recip. of '1' -
('c'+'d'+'f'+'g'+'h')... At least that the value I'm looking for is
simply the one calculated in 'e'?
I know the question has been asked many times. But I am still confused
after have read all the answers... A tutorial about that would be great!
Thanks in advance for your comments
Nicolas
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fn:Nicolas SAPAY
n:SAPAY;Nicolas
org:University of Calgary;Biological Sciences
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
email;internet:[EMAIL PROTECTED]
title:PhD
tel;work:(403) 220-6869
tel;fax:(403) 289-9311
x-mozilla-html:TRUE
version:2.1
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[gmx-users] To deshuffle or not to deshuffle, that is a question.
Hi guys, A stupid question: I got myself confused with this shuffling/deshuffling thing, which I shouldn't have been doing with protein in the first place. So this are my steps, done on the same 4 nodes, please tell me whether I was supposed to do any deshuffling of .trr and .gro files, and following which steps: 1)minimization, supplied output .gro to the next step 2)equilibration, supplied output .gro to the next step 3) NVT run, supplied output .gro and .trr to the next step 4) NPT run A simple YES or NO for each step will suffice. Thanks, Frankie ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Structural alignment of different proteins
Dear GMX users, I uploaded a wrapper to run the Multiprot program using output from Gromacs to the user contributions in the GMX site. Multiprot, http://bioinfo3d.cs.tau.ac.il/MultiProt/ , performs structural alignment based on geometry, not sequence, and thus it allows the alignment of two proteins that differ in sequence. The alignment is performed over a subset of the atoms which geometrically match. The wrapper program, do_multipriot, uses multiprot to calculate the rms between the trajectory and a reference protein and gives the number of aligned residues as well. It's also possible to extract the aligned trajectory. As in the case of do_dssp, multiprot is not distributed in the contribution since it's not gpl. However, it is free for academic users and can be downloaded from the multiprot site. Hope other users will find this useful. Ran. -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
