Compiling GROMACS w CUDA 5.0 problem I did this a few days. i will share my how to do. i used gromacs 4.6.1. assuming u have the nvidia gpu also
1.$ tar xfz gromacs-4.6.tgz $ cd gromacs-4.6 $ mkdir build-cmake $ cd build-cmake $sudo apt-get install cmake $ cmake .. $cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda sudo apt-get install libfftw3-dev libfftw3-doc $ CMAKE_PREFIX_PATH=/opt/fftw:/opt/cuda cmake .. $cmake .. -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_mod -DGMX_LIBS_SUFFIX=_mod $ make -j 8$make install $ source /usr/local/gromacs/bin/GMXRC Running the file: give the following input in the mdp file cutoff-scheme = Verlet regards ayesha On Mon, May 27, 2013 at 6:00 PM, <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > 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 > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Entropy (Yulian) > 2. Re: g_hbond (maggin) > 3. Re: mdrun outputs incorrect resnames (Reid Van Lehn) > 4. AMBER99 P450 heme topology (Parker de Waal) > 5. Compiling GROMACS w CUDA 5.0 problem (Jernej Zidar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 26 May 2013 05:04:59 -0700 (PDT) > From: Yulian <[email protected]> > Subject: [gmx-users] Entropy > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=us-ascii > > Dear Gromacs users, > There is a problem with entropy calculations with g_anaeig. > > I have 3 runs 100 ns each. > Entropy for each run (Protein-H) is round 31000 J/mol K (100 ns) > If I use trjcat to connect two trajectories it is 26000 J/mol K (200 ns) > For three connect trajectories it is round 19000 J/mol K > > > I tried to do some checking: > For example, I used 50 ns from one traj and 50 ns from the other in > different combinations but it does not change the entropy value > significantly. It seems that three runs are not so different. > > Also there is a problem with calculating of entropy on different machines. > The result can be different for different machines (+/- several hundreds > of > J/mol K for this system) > > I use gromacs-4.5.6. > For all runs I use "trjconv -pbc nojump" before analysis. > Thank you. > > Yulian > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Entropy-tp5008547.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 2 > Date: Sun, 26 May 2013 07:23:56 -0700 (PDT) > From: maggin <[email protected]> > Subject: [gmx-users] Re: g_hbond > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=us-ascii > > Hi, Erik > > Thank you very much!Thank you! > > maggin > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507p5008548.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 3 > Date: Sun, 26 May 2013 13:21:55 -0400 > From: Reid Van Lehn <[email protected]> > Subject: Re: [gmx-users] mdrun outputs incorrect resnames > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > < > cal_famm2ux_osqtsmmscd_fqgzd+c4cwrptgxen8udro2c4...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Great, thank you that did the trick. My fault for not realizing this > earlier. > > Best, > Reid > > > On Sun, May 26, 2013 at 2:12 AM, Tsjerk Wassenaar <[email protected]> > wrote: > > > No, the residue names are the those from the .top file. But that's not > the > > same as the moleculetypes. You have to change the residue names in the [ > > atoms ] section. > > > > Cheers, > > > > Tsjerk > > > > > > On Sun, May 26, 2013 at 12:57 AM, Mark Abraham <[email protected] > > >wrote: > > > > > AFAIK, the residue names in the mdrun output .gro file are those of the > > > structure file you gave to grompp. > > > > > > Mark > > > > > > > > > On Sun, May 26, 2013 at 12:31 AM, Reid Van Lehn <[email protected]> > > > wrote: > > > > > > > Hello, > > > > > > > > I am simulating a lipid bilayer and wish to apply position restraints > > to > > > > only a subset of the lipids in the bilayer. Since position restraints > > are > > > > applied to all molecules of the same molecule type, I defined a new > > > > molecule type (DOPR) which is identical to my lipid species (DOPC) by > > > > copying the lipid itp file, renaming it and renaming the > corresponding > > > > molecule type. I then manually edited a starting .gro file to change > a > > > > subset of the DOPC molecules to DOPR, edited my topology, > > > > renumbered/reordered, etc. I also recreated the index file to account > > for > > > > the new molecules so that temperature coupling could be used > correctly. > > > > > > > > Everything seemed ok when I ran the mdrun - grompp didn't complain, > the > > > > program ran normally, the output trajectory clearly used the correct > > > > position restraints, etc. The weird part, though, is that the output > > .gro > > > > file at the end of the simulation only had DOPC molecules in it - the > > > DOPR > > > > molecules that I had renamed by hand had somehow been output as DOPC > > > > instead. Positions, number of atoms, everything else was fine, just > the > > > > name of the residues was different. I can't figure out why this is > > > > happening. It was reproducible across both GMX 4.5.5 / 4.6 and > multiple > > > > different starting files. > > > > > > > > It's not a huge issue since the trajectories themselves are fine, I'm > > > just > > > > worried this issue might indicate other, less obvious problems. A > > snippet > > > > of the topol file is below if that is helpful. > > > > > > > > Any suggestions / advice would be appreciated! > > > > > > > > ******************************** > > > > #include "forcefield.itp > > > > #include "dopc.itp" > > > > > > > > #ifdef POSRES > > > > #include "dopc-posre.itp" > > > > #endif > > > > > > > > ; Always include DOPR restraints for restrained lipids > > > > #include "dopc_restrained.itp" > > > > #include "dopr-posre.itp" > > > > > > > > #include "spc.itp" > > > > #include "ions.itp" > > > > > > > > [ system ] > > > > ; Name > > > > frame t= 1.000 in water > > > > > > > > [ molecules ] > > > > ; Compound #mols > > > > DOPC 398 > > > > DOPR 2 > > > > SOL 63882 > > > > NA 179 > > > > CL 179 > > > > ********************************* > > > > > > > > Thanks, > > > > Reid > > > > -- > > > > gmx-users mailing list [email protected] > > > > 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 [email protected]. > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > -- > > > gmx-users mailing list [email protected] > > > 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 [email protected]. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > -- > > gmx-users mailing list [email protected] > > 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 [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Reid Van Lehn > NSF/MIT Presidential Fellow > Alfredo Alexander-Katz Research Group > Ph.D Candidate - Materials Science > > > ------------------------------ > > Message: 4 > Date: Sun, 26 May 2013 21:36:53 -0400 > From: Parker de Waal <[email protected]> > Subject: [gmx-users] AMBER99 P450 heme topology > To: <[email protected]> > Message-ID: > < > caj0kcuet0qbnjb9ie5jfjmo0qn9urblhdxzfojomuy5u6ac...@mail.gmail.com> > Content-Type: text/plain; charset="ISO-8859-1" > > Hi Everyone, > > I've been looking running MD simulations on heme containing P450s using the > AMBER99 force field however have bee having a hard time generating or > finding a usable topology file for the heme cofactor. > > Does anyone have any recommendations for heme topology files and how to use > them? > > Thanks! > Parker! > > > ------------------------------ > > Message: 5 > Date: Mon, 27 May 2013 13:34:02 +0800 > From: Jernej Zidar <[email protected]> > Subject: [gmx-users] Compiling GROMACS w CUDA 5.0 problem > To: [email protected] > Message-ID: > < > caanrtrkjdohshz_xf+cdgzy8tgvku_tjwrehawxsmkksr4b...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi, > I want to compile GROMACS to support CUDA. > > First I do a cmake: > CMAKE_PREFIX_PATH=/scratch/ihpc/ihpczidj/local/bin/:/usr/local/CUDA/5.0/ > cmake ../gromacs-4.6 -DGMX_GPU=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF > -DGMX_OPENMP=ON -DBUILD_SHARED_LIBS=OFF > -DCMAKE_INSTALL_PREFIX=/scratch/ihpc/ihpczidj/local/gromacs-4.6-ompi-cuda > -DCMAKE_CXX_COMPILER=/scratch/ihpc/ihpczidj/local/bin/mpicxx > -DCMAKE_C_COMPILER=/scratch/ihpc/ihpczidj/local/bin/mpicc > -DGMX_BUILD_OWN_FFTW=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/CUDA/5.0/ > > Then I do a 'make' which completes without a problem. The problem is > that when I issue a 'make install' the whole compilation process > starts again and fails stating: > -- The GROMACS-managed build of FFTW 3 will configure with the > following optimizations: --enable-sse2 > -- Configuring done > You have changed variables that require your cache to be deleted. > Configure will be re-run and you may have to reset some variables. > The following variables have changed: > CMAKE_C_COMPILER= /home1/ihpc/ihpczidj/scratch/local/bin/mpicc > CMAKE_CXX_COMPILER= /home1/ihpc/ihpczidj/scratch/local/bin/mpicxx > > Between the 'cmake', 'make' and 'make install' steps I made no > changes to neither of the variables. > > The error is unrelated to the use of Open MPI as I get the same > error when if I compile using threads. > > I'm using GCC 4.6.3 and CUDA 5.0. > > Any advice? > > Thanks, > Jernej > > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 109, Issue 153 > ******************************************* > -- gmx-users mailing list [email protected] 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. 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