Re: [gmx-users] Failing installation with --enable-mpi option
Dear Justin, could you please write what environmental changes you made to MPICC.. I tried to alter the profile, but it is rejecting all of them.. Bhanu. On 20/05/2009, Bhanu bhanui...@gmail.com wrote: Thanks Justin, will try your suggestion.. 2009/5/20 Justin A. Lemkul jalem...@vt.edu: Bhanu wrote: I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix=_mpi it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix=_mpi checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /bin/sh: /home/sandaka/Desktop/all: No such file or directory configure: WARNING: `missing' script is too old or missing 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 catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. Am attaching the config.log file herein. I've Openmpi and fftw already installed and in the path.. Couldn't understand what is the error! Have a look at this thread: http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html -Justin ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://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 -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ 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
Re: [gmx-users] Failing installation with --enable-mpi option
Bhanu wrote: Dear Justin, could you please write what environmental changes you made to MPICC.. I tried to alter the profile, but it is rejecting all of them.. mpicc is only one theory for the problem, as I explain deep in the thread Justin linked. Try configuring without --enable-mpi to test Justin's theory. You providing us with more information about your system and OS would help us diagnose. Also, you should spend your time installing the latest GROMACS, not one from months ago. Mark On 20/05/2009, Bhanu bhanui...@gmail.com wrote: Thanks Justin, will try your suggestion.. 2009/5/20 Justin A. Lemkul jalem...@vt.edu: Bhanu wrote: I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix=_mpi it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix=_mpi checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /bin/sh: /home/sandaka/Desktop/all: No such file or directory configure: WARNING: `missing' script is too old or missing 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 catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. Am attaching the config.log file herein. I've Openmpi and fftw already installed and in the path.. Couldn't understand what is the error! Have a look at this thread: http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html -Justin ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://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 -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ 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
Re: [gmx-users] Test suit failures
Bert wrote: Dear gmx-users, I have done a test using test suit 4.0.4, and I got some failures as follows. All 16 simple tests PASSED FAILED. Check files in aminoacids FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check files in water Those fail frequently on normal installations because they are susceptible to differences in the virial. 4 out of 14 complex tests FAILED FAILED. Check files in kernel020 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 16 out of 63 kernel tests FAILED These are caused by a known bug in GROMACS. All 45 pdb2gmx tests PASSED My gcc version is 4.1.1, and both gmx 4.0.4 and 4.0.5 get exactly the same failures on my Xeon 8 core based linux. For example, in /kernel/kernel020 You'll probably be fine if you either upgrade your gcc version or learn that your particular 4.1.x series compiler has its bugs fixed. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: Lipids forming unsual bonds
Hi Dallas, Mark Chris, Thanks a lot for your replies. Yes, the problem was due to visualization artifacts and was solved by using the dynamic bonds representation of VMD. Thanks a lot. Regards, Anirban GhoshGrade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com___ 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
[gmx-users] mdp file to calculate local pressure
Dear Sir, I want to calculate local pressure of the membrane (pressure variation with z -axis). I am using gromacs-localp packages. As I see that all types of errors coming from saying specifically the option of WALL in .mdp file. Actually I did not understand clearly what to do in the following options. WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 Could you please write clearly what to write on above options ?? I am writing here the mdp file what I am using in gromacs-localp package to calculate local pressure. integrator = sd ; stochastic dynamics - Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps = 5 ; total 500/5=100 ps nstcomm = 1 ; freq. for cm-motion removal tinit= 0 ; starting time (ps) constraints = all-bonds ; constraint for all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default nstxout = 1000; T(x_out) 10 ps nstvout = 1000; T(v_out) 10 ps nstfout = 0 ; T(f_out) nstlog = 250 ; energies to log (0.5 ps) nstenergy= 250 ; energies to energy file ns_type = grid; nl type nstlist = 10 ; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range nl) ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy coulombtype = PME ;Reaction-Field ; Coulomb interactions rcoulomb = 1.0 ;2.0 ; nm (Coulomb cut-off!!) epsilon_r= 80.0; dielectric constant for reaction field vdwtype = Cut-off ; Wan der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) optimize_fft = yes ; Temperature coupling Tcoupl = no ; no effect when integrator = sd tc-grps = POPC SM CHOL SOL tau_t= 0.1 0.1 0.1 0.1 ref_t= 296 296 296 296 ; Pressure coupling ;Pcoupl = no Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 1.01.0 ; ps compressibility = 4.5e-5 4.5e-5; 1/bar (water: 1 atm, 300 K) ref_p= 1.01.0 ; bar ; Generate velocites in the beginning gen_vel = yes gen_temp = 296.0 gen_seed = 173529 ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 Thanks a lot in advance. Regards, Anirban ___ 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
Re: [gmx-users] mdp file to calculate local pressure
anirban polley wrote: Dear Sir, I want to calculate local pressure of the membrane (pressure variation with z -axis). I am using gromacs-localp packages. As I see that all types of errors coming from saying specifically the option of WALL in .mdp file. Actually I did not understand clearly what to do in the following options. The simple answer to me is - why are you using walls? The gromacs-localp package is based on version 3.0.2, and IIRC walls were introduced much later in development, probably version 4.0. At least, there is no mention of walls in any documentation prior to the 4.0 manual. -Justin WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 Could you please write clearly what to write on above options ?? I am writing here the mdp file what I am using in gromacs-localp package to calculate local pressure. integrator = sd ; stochastic dynamics - Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps = 5 ; total 500/5=100 ps nstcomm = 1 ; freq. for cm-motion removal tinit= 0 ; starting time (ps) constraints = all-bonds ; constraint for all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default nstxout = 1000; T(x_out) 10 ps nstvout = 1000; T(v_out) 10 ps nstfout = 0 ; T(f_out) nstlog = 250 ; energies to log (0.5 ps) nstenergy= 250 ; energies to energy file ns_type = grid; nl type nstlist = 10 ; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range nl) ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy coulombtype = PME ;Reaction-Field ; Coulomb interactions rcoulomb = 1.0 ;2.0 ; nm (Coulomb cut-off!!) epsilon_r= 80.0; dielectric constant for reaction field vdwtype = Cut-off ; Wan der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) optimize_fft = yes ; Temperature coupling Tcoupl = no ; no effect when integrator = sd tc-grps = POPC SM CHOL SOL tau_t= 0.1 0.1 0.1 0.1 ref_t= 296 296 296 296 ; Pressure coupling ;Pcoupl = no Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 1.01.0 ; ps compressibility = 4.5e-5 4.5e-5; 1/bar (water: 1 atm, 300 K) ref_p= 1.01.0 ; bar ; Generate velocites in the beginning gen_vel = yes gen_temp = 296.0 gen_seed = 173529 ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 Thanks a lot in advance. Regards, Anirban ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://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
[gmx-users] in vacuo minimization of a multimeric protein
Dear gmx-users, I'm trying to do a mild minimization on a homohexameric protein in vacuo. I used the following options in the em.mdp file: title = mild-mini cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 500 emtol = 5000 emstep = 0.1 nstcomm = 1 ns_type = grid nstlist = 5 rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes I simply converted my protein from .pdb format to .gro using pdb2gmx, and then I submitted immediately to minimization, since I only would like to relieve some eventual steric clashes between subunits, without proceed with a further MD simulation and without distorting too much the protein structure. At the end of the run I found that the 6 subunits of my protein (which are not covalently linked to each others) are separated in two dimers and two monomers. I tried also the minimization in water, although for this system I don't want water, but the result is not changing: the protein separates in subunits. The same if I apply PBC (the first time I applied it, then I saw that the subunits separated, I check the gmx-users list and delete pbc from the em.mdp, but the results are quite the same). I also changed ns_type to simple, without success. Have you got any suggestion? Thanks in advance Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you are too small to make a difference, try sleeping with a mosquito ___ 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
Re: [gmx-users] in vacuo minimization of a multimeric protein
Anna Marabotti wrote: Dear gmx-users, I'm trying to do a mild minimization on a homohexameric protein in vacuo. I used the following options in the em.mdp file: title = mild-mini cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 500 emtol = 5000 emstep = 0.1 nstcomm = 1 ns_type = grid nstlist = 5 rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes I simply converted my protein from .pdb format to .gro using pdb2gmx, and then I submitted immediately to minimization, since I only would like to relieve some eventual steric clashes between subunits, without proceed with a further MD simulation and without distorting too much the protein structure. At the end of the run I found that the 6 subunits of my protein (which are not covalently linked to each others) are separated in two dimers and two monomers. I tried also the minimization in water, although for this system I don't want water, but the result is not changing: the protein separates in subunits. The same if I apply PBC (the first time I applied it, then I saw that the subunits separated, I check the gmx-users list and delete pbc from the em.mdp, but the results are quite the same). I also changed ns_type to simple, without success. Have you got any suggestion? Thanks in advance If you have gone straight from pdb2gmx to grompp, then your box size is likely inappropriate. Use editconf -c -d to define a suitably large box. -Justin Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabo...@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you are too small to make a difference, try sleeping with a mosquito ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://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
[gmx-users] bond, angle and dihedral restraints in Gromacs
Hello, I would like to simulate a CNT and I want to apply a harmonic potential: -on the C-C bonds -on the bond angles -on the dihedral angles with a different spring constant for each case. I have read Section 4.3 from Gromacs manual, but I actually have some doubts about how to include this in the topology. -for the distance restraints I have tried to use genrestr: genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 40 The file I obtain is something like: ; distance restraints for UNK of cnt_wat_gmx.gro created by rdparm2gmx.pl Wed May 20 10:20:59 BST 2009 [ distance_restraints ] ; i j ? label funct loup1up2 weight 1 2 1 0 1 0.403354 0.6033541.60335 1 1 3 1 1 1 0.587676 0.7876761.78768 1 1 4 1 2 1 0.769212 0.9692121.96921 1 1 5 1 3 10.860811.060812.06081 1 (...) This is different from the [distance_restraint] example shown in pag 69 of the manual, now I don' t have the fac column. I would like to apply a spring constant of 40 to C-C bonds, but where is the constant here? How could I apply a determined spring constant? In the .mdp file? Besides, all the distances are restrained... Is there any way to restrain only the C-C bonds? I mean I don' t want to restrain the distance between a carbon and a carbon far away from it, only restraining the neighbouring carbons to a distance of 1.4 A. Another question is: Is there any tool to construct the equivalent angle_restraints and dihedral_restraints in an authomatic way, or should I do it by hand? Thank you very much in advance for your help. Best wishes, Dr. Rebeca Garcia Parc Cientific de Barcelona Spain _ ¡Quítate unos clics! Ahora, Internet Explorer 8 tiene todo lo que te gusta de Windows Live ¡Consíguelo gratis! http://ie8.msn.com/microsoft/internet-explorer-8/es-es/ie8.aspx___ 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
Re: [gmx-users] bond, angle and dihedral restraints in Gromacs
Rebeca García Fandiño wrote: Hello, I would like to simulate a CNT and I want to apply a harmonic potential: -on the C-C bonds -on the bond angles -on the dihedral angles with a different spring constant for each case. I have read Section 4.3 from Gromacs manual, but I actually have some doubts about how to include this in the topology. -for the distance restraints I have tried to use genrestr: genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 40 The file I obtain is something like: ; distance restraints for UNK of cnt_wat_gmx.gro created by rdparm2gmx.pl Wed May 20 10:20:59 BST 2009 [ distance_restraints ] ; i j ? label funct loup1up2 weight 1 2 1 0 1 0.403354 0.6033541.60335 1 1 3 1 1 1 0.587676 0.7876761.78768 1 1 4 1 2 1 0.769212 0.9692121.96921 1 1 5 1 3 10.860811.060812.06081 1 (...) This is different from the [distance_restraint] example shown in pag 69 of the manual, now I don' t have the fac column. I would like to apply a The format of the distance_restraints section appears correct. If you read the description of the fac column, it is a weighting factor for that particular restraint. So therefore, weight is probably equivalent. spring constant of 40 to C-C bonds, but where is the constant here? How could I apply a determined spring constant? In the .mdp file? Besides, all the distances are restrained... Is there any way to restrain only the C-C bonds? I mean I don' t want to restrain the distance between a carbon and a carbon far away from it, only restraining the neighbouring carbons to a distance of 1.4 A. You cannot use genrestr for this purpose. Using genrestr -disre generates a matrix of all atoms you specify. Also, -fc is expected to be used with position restraints; note the format given in genrestr -h. Are you really interested in applying restraints to all bonds, angles, dihedrals, and distances? Realize that constraints (Section 5.5) and restraints are separate ideas in Gromacs. If you want to define your own force constants for bonds, angles, etc. simply do so in the topology yourself (Table 5.4). -Justin Another question is: Is there any tool to construct the equivalent angle_restraints and dihedral_restraints in an authomatic way, or should I do it by hand? Thank you very much in advance for your help. Best wishes, Dr. Rebeca Garcia Parc Cientific de Barcelona Spain Haz búsquedas con Live Search, ¡todas tus búsquedas tienen premio! http://www.buscalasuerte.com/ ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://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
[gmx-users] topology of HEO compound in .rtp for G96 ff
Hello, could anyone help me and check if the topology of the HEO compound was done properly for G96 ff? Thanks in advance. I couldn't find it in the database, so I decided to try to make it manualy. Any comments would be appreciated. Or maybe does exists any programs who does the work? [ HEO ] [ atoms ] FEFE 0.4 0 NANR-0.1 0 NBNR-0.1 0 NCNR-0.1 0 NDNR-0.1 0 CHA CH1 0.0 1 C1A C 0.0 2 C2A C 0.0 2 C3A C 0.0 2 C4A C 0.0 2 CMA CH3 0.0 3 CAA CH2 0.0 4 CBA CH2 0.0 4 CGA C 0.27000 5 O1AOM-0.63500 5 O2AOM-0.63500 5 CHB CH1 0.0 6 C1B C 0.0 7 C2B C 0.0 7 C3B C 0.0 7 C4B C 0.0 7 CMB CH3 0.0 8 C11 C 0.38000 9 O11 O-0.38000 9 CHC CH1 0.010 C1C C 0.011 C2C C 0.011 C3C C 0.011 C4C C 0.011 CMC CH3 0.012 CAC CR1 0.013 CBC CH2 0.013 CHD CH1 0.014 C1D C 0.015 C2D C 0.015 C3D C 0.015 C4D C 0.015 CMD CH3 0.016 CAD CH2 0.017 CBD CH2 0.017 CGD C 0.2700018 O1DOM-0.6350018 O2DOM-0.6350018 C12 CH2 0.019 C13 CH2 0.019 C14 CH2 0.020 C15 CH1 0.020 C16 CH3 0.020 C17 CH2 0.020 C18 CH2 0.021 C19 CH2 0.022 C20 CH1 0.022 C21 CH3 0.022 C22 CH2 0.022 C23 CH2 0.023 C24 CH2 0.024 C25 CH1 0.024 C26 CH3 0.024 C27 CH3 0.024 [ bonds ] FENAgb_34 FENBgb_34 FENCgb_34 FENDgb_34 NA C1Agb_13 NA C4Agb_13 NB C1Bgb_13 NB C4Bgb_13 NC C1Cgb_13 NC C4Cgb_13 ND C1Dgb_13 ND C4Dgb_13 CHA C1Agb_16 CHA C4Dgb_16 C1A C2Agb_16 C2A C3Agb_16 C2A CAAgb_26 C3A C4Agb_16 C3A CMAgb_26 C4A CHBgb_16 CAA CBAgb_26 CBA CGAgb_26 CGA O1Agb_5 CGA O2Agb_5 CHB C1Bgb_16 C1B C2Bgb_16 C2B C3Bgb_16 C2B CMBgb_26 C3B C4Bgb_16 C4B CHCgb_16 CHC C1Cgb_16 C1C C2Cgb_16 C2C C3Cgb_16 C2C CMCgb_26 C3C C4Cgb_16 C3C CACgb_26 C4C CHDgb_16 CAC CBCgb_11 CHD C1Dgb_16 C1D C2Dgb_16 C2D C3Dgb_16 C2D CMDgb_26 C3D C4Dgb_16 C3D CADgb_26 CAD CBDgb_26 CBD CGDgb_26 CGD O1Dgb_5 CGD O2Dgb_5 C3B C11gb_26 C11 O11gb_4 C11 C12gb_26 ; C, CHn - C, CHn800 C12 C13gb_26 ; C, CHn - C, CHn800 C13 C14gb_26 ; C, CHn - C, CHn800 C14 C15gb_26 ; C, CHn - C, CHn800 C15 C16gb_26 ; C, CHn - C, CHn800 C15 C17gb_26 ; C, CHn - C, CHn800 C17 C18gb_26 ; C, CHn - C, CHn800 C18 C19gb_26 ; C, CHn - C, CHn800 C19 C20gb_26 ; C, CHn - C, CHn800 C20 C21gb_26 ; C, CHn - C, CHn800 C20 C22gb_26 ; C, CHn - C, CHn800 C22 C23gb_26 ; C, CHn - C, CHn800 C23 C24gb_26 ; C, CHn - C, CHn800 C24 C25gb_26 ; C, CHn - C, CHn800 C25 C26gb_26 ; C, CHn - C, CHn800 C25 C27gb_26 ; C, CHn - C, CHn800 [ exclusions ] ; aiaj FE CHA FE C2A FE C3A FE CHB FE C2B FE C3B FE CHC FE C2C FE C3C FE CHD FE C2D FE C3D NA CMA NA CAA NA C1B NA C4B NA C1C NA C4C NA C1D NA C4D NB C1A NB C4A NB CMB NB C11 NB C1C NB C4C NB C1D NB C4D NC C1A NC C4A NC C1B NC C4B NC CMC NC CAC NC C1D NC C4D ND C1A ND C4A ND C1B ND C4B ND C1C ND C4C ND CMD ND CAD CHA C3A CHA C4A CHA CAA CHA C1D CHA C2D CHA CAD C1A CMA C1A CHB C1A C3D C2A CHB C3A C1B C4A CAA C4A C2B CMA CAA CMA CHB CHB C3B CHB C4B CHB CMB C1B C11 C1B CHC C2B CHC C3B C1C C4B CMB C4B C2C CMB C11 C11 CHC CHC C3C CHC C4C CHC
Re: [gmx-users] topology of HEO compound in .rtp for G96 ff
Egidijus Kuprusevicius wrote: Hello, could anyone help me and check if the topology of the HEO compound was done properly for G96 ff? Thanks in advance. I couldn't find it in the database, so I decided to try to make it manualy. Any comments would be appreciated. Or maybe does exists any programs who does the work? It would help to know what HEO is, and which version of Gromos96 you are attempting to use. If this is some sort of HEME derivative, as it appears, you can probably verify much of the topology, since HEME exists in the .rtp file for all the Gromos96 variants. It is not possible to simply look at a topology and verify if it is correct. Parameterization requires you to verify some sort of experimental observable to justify the parameters you have assigned. -Justin [ HEO ] [ atoms ] FEFE 0.4 0 NANR-0.1 0 NBNR-0.1 0 NCNR-0.1 0 NDNR-0.1 0 CHA CH1 0.0 1 C1A C 0.0 2 C2A C 0.0 2 C3A C 0.0 2 C4A C 0.0 2 CMA CH3 0.0 3 CAA CH2 0.0 4 CBA CH2 0.0 4 CGA C 0.27000 5 O1AOM-0.63500 5 O2AOM-0.63500 5 CHB CH1 0.0 6 C1B C 0.0 7 C2B C 0.0 7 C3B C 0.0 7 C4B C 0.0 7 CMB CH3 0.0 8 C11 C 0.38000 9 O11 O-0.38000 9 CHC CH1 0.010 C1C C 0.011 C2C C 0.011 C3C C 0.011 C4C C 0.011 CMC CH3 0.012 CAC CR1 0.013 CBC CH2 0.013 CHD CH1 0.014 C1D C 0.015 C2D C 0.015 C3D C 0.015 C4D C 0.015 CMD CH3 0.016 CAD CH2 0.017 CBD CH2 0.017 CGD C 0.2700018 O1DOM-0.6350018 O2DOM-0.6350018 C12 CH2 0.019 C13 CH2 0.019 C14 CH2 0.020 C15 CH1 0.020 C16 CH3 0.020 C17 CH2 0.020 C18 CH2 0.021 C19 CH2 0.022 C20 CH1 0.022 C21 CH3 0.022 C22 CH2 0.022 C23 CH2 0.023 C24 CH2 0.024 C25 CH1 0.024 C26 CH3 0.024 C27 CH3 0.024 [ bonds ] FENAgb_34 FENBgb_34 FENCgb_34 FENDgb_34 NA C1Agb_13 NA C4Agb_13 NB C1Bgb_13 NB C4Bgb_13 NC C1Cgb_13 NC C4Cgb_13 ND C1Dgb_13 ND C4Dgb_13 CHA C1Agb_16 CHA C4Dgb_16 C1A C2Agb_16 C2A C3Agb_16 C2A CAAgb_26 C3A C4Agb_16 C3A CMAgb_26 C4A CHBgb_16 CAA CBAgb_26 CBA CGAgb_26 CGA O1Agb_5 CGA O2Agb_5 CHB C1Bgb_16 C1B C2Bgb_16 C2B C3Bgb_16 C2B CMBgb_26 C3B C4Bgb_16 C4B CHCgb_16 CHC C1Cgb_16 C1C C2Cgb_16 C2C C3Cgb_16 C2C CMCgb_26 C3C C4Cgb_16 C3C CACgb_26 C4C CHDgb_16 CAC CBCgb_11 CHD C1Dgb_16 C1D C2Dgb_16 C2D C3Dgb_16 C2D CMDgb_26 C3D C4Dgb_16 C3D CADgb_26 CAD CBDgb_26 CBD CGDgb_26 CGD O1Dgb_5 CGD O2Dgb_5 C3B C11gb_26 C11 O11gb_4 C11 C12gb_26 ; C, CHn - C, CHn800 C12 C13gb_26 ; C, CHn - C, CHn800 C13 C14gb_26 ; C, CHn - C, CHn800 C14 C15gb_26 ; C, CHn - C, CHn800 C15 C16gb_26 ; C, CHn - C, CHn800 C15 C17gb_26 ; C, CHn - C, CHn800 C17 C18gb_26 ; C, CHn - C, CHn800 C18 C19gb_26 ; C, CHn - C, CHn800 C19 C20gb_26 ; C, CHn - C, CHn800 C20 C21gb_26 ; C, CHn - C, CHn800 C20 C22gb_26 ; C, CHn - C, CHn800 C22 C23gb_26 ; C, CHn - C, CHn800 C23 C24gb_26 ; C, CHn - C, CHn800 C24 C25gb_26 ; C, CHn - C, CHn800 C25 C26gb_26 ; C, CHn - C, CHn800 C25 C27gb_26 ; C, CHn - C, CHn800 [ exclusions ] ; aiaj FE CHA FE C2A FE C3A FE CHB FE C2B FE C3B FE CHC FE C2C FE C3C FE CHD FE C2D FE C3D NA CMA NA CAA NA C1B NA C4B NA C1C NA C4C NA C1D NA C4D NB C1A NB C4A NB CMB NB C11 NB C1C NB C4C NB C1D NB C4D NC C1A NC
[gmx-users] grompp 4.0.5 hangs while 3.2.1 works
I have a system which works with grompp 3.2.1 but grompp 4.0.5 hangs at ‘processing topology...’. Is there something that had changed (say, file format in .top or .itp) that could have caused this? I can supply my topology, conformation, etc. files if necessary for debugging. Cheers. $ grompp -v -f test0_.mdp -po test0.mdp -c initial.gro -p Kir21.top -o test0.tpr :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -f test0_.mdp Input, Opt! grompp input file with MD parameters -po test0.mdp Output grompp input file with MD parameters -cinitial.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p Kir21.top InputTopology file -pp processed.top Output, Opt. Topology file -o test0.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up test0.mdp to ./#test0.mdp.7# checking input for internal consistency... NOTE 1 [file test0_.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. ERROR: With coulombtype = PME, rcoulomb must be equal to rlist If you want optimal energy conservation or exact integration use PME-Switch processing topology... ___ 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
Re: [gmx-users] grompp 4.0.5 hangs while 3.2.1 works
Kaihsu Tai wrote: I have a system which works with grompp 3.2.1 but grompp 4.0.5 hangs at ‘processing topology...’. Is there something that had changed (say, file format in .top or .itp) that could have caused this? I can supply my topology, conformation, etc. files if necessary for debugging. Cheers. $ grompp -v -f test0_.mdp -po test0.mdp -c initial.gro -p Kir21.top -o test0.tpr :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -f test0_.mdp Input, Opt! grompp input file with MD parameters -po test0.mdp Output grompp input file with MD parameters -cinitial.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p Kir21.top InputTopology file -pp processed.top Output, Opt. Topology file -o test0.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up test0.mdp to ./#test0.mdp.7# checking input for internal consistency... NOTE 1 [file test0_.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. ERROR: With coulombtype = PME, rcoulomb must be equal to rlist If you want optimal energy conservation or exact integration use PME-Switch processing topology... ___ 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 Please submit a bugzilla with all input files to reproduce the problem. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdp file to calculate local pressure
Dear Justin, I am using gromacs-localp of version 4.0.2. for the calculation of local pressure. But I could not understand what I should put in the mdp file. Because when I tried by the following below mdp file, it does not even create tpr file. I have tried by different options as for example by using Wall but failed to get local pressure profile. I thought that I have write some thing so that it can be ok for giving local pressure. Could you please correct my mdp file and write what extra term I should write in my mdp file to get local pressure. Thank you very much for your kind help. Anirban title= lipid bilayer in water cpp = /lib/cpp integrator = sd ; stochastic dynamics - Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps = 25 ; total 500 ps nstcomm = 1 ; freq. for cm-motion removal tinit= 0 ; starting time (ps) constraints = all-bonds ; constraint for all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default nstxout = 5000; T(x_out) 10 ps nstvout = 5000; T(v_out) 10 ps nstfout = 0 ; T(f_out) nstlog = 250 ; energies to log (0.5 ps) nstenergy= 250 ; energies to energy file ns_type = grid; nl type nstlist = 10 ; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range nl) coulombtype = Reaction-Field ; Coulomb interactions rcoulomb = 2.0 ; nm (Coulomb cut-off!!) epsilon_r= 80.0; dielectric constant for reaction field vdwtype = Cut-off ; Wan der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) optimize_fft = yes ; Temperature coupling Tcoupl = no ; no effect when integrator = sd tc-grps = POPC SMCHOL SOL tau_t= 0.1 0.1 0.1 0.1 ref_t= 296 296 296 296 ; Pressure coupling ;Pcoupl = no Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 1.01.0 ; ps compressibility = 4.5e-5 4.5e-5; 1/bar (water: 1 atm, 300 K) ref_p= 1.01.0 ; bar ; Generate velocites in the beginning gen_vel = yes gen_temp = 296.0 gen_seed = 173529 ___ 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
[gmx-users] problem in removal of unwanted water from hydrophobic core of lipid bilayer
Dear all
I am running keepbyz.pl script to remove unwanted
waters from hydrophobic core of lipid . I am getting problem in this
process. For this I follow the chris neale rule -
*1. run genbox on initial.gro to create solvated.gro
** 2. cp solvated.gro new_waters.gro
** 3. use vi to remove everything in new_waters.gro except the new waters (make
** sure you remove waters that were in initial.gro)
** 4. use vi to edit keepbyz.pl
**- upperz and lowerz variables as you please
**- sol to the name of your solvent molecule
** 5. run keepbyz.pl on new_waters.gro
**./keepbyz new_waters.gro keep_these_waters.gro
** 6. tail -1 initial.gro last_line.gro
** 7. head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1
) initial.gro
**
** not_last_line.gro
**
** 8. cat not_last_line.gro new_waters.gro last_line.gro new_system.gro
** 9. editconf -f new_system.gro -o new_system_sequential_numbers.gro
*
I have successfully completed all the step but getting problem in completing
last step i.e editconf step , in the last file new_sequential_numbers.gro
which is made by editconf unable to keep solvent molecules which is present
in new_system.gro . Also one warning came during the last editconf process
i.e-
WARNING 1 [file aminoacids.dat, line 1]:
Bad box in file new_system.gro
I am unable to understand why it shows Bad box in file new_system.gro ?.
Can anyone help me to solve this problem.?
I will be really thankful for that.
Nitu sharma.
___
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