[gmx-users] Re: gmx-users Digest, Vol 109, Issue 153

[Ayesha Fatima]

 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, <gmx-users-request at gromacs.org> wrote:

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> 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 <zzeppelin87 at gmail.com>
> Subject: [gmx-users] Entropy
> To: gmx-users at gromacs.org
> Message-ID: <1369569899419-5008547.post at n6.nabble.com>
> 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 <maggin.chen at gmail.com>
> Subject: [gmx-users] Re: g_hbond
> To: gmx-users at gromacs.org
> Message-ID: <1369578236451-5008548.post at n6.nabble.com>
> 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 <rvanlehn at gmail.com>
> Subject: Re: [gmx-users] mdrun outputs incorrect resnames
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <
> CAL_FAMM2ux_osQTSMMscD_fqgzD+c4CWrPtgxEn8uDrO2c4k1A at 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 <tsjerkw at gmail.com>
> 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 <mark.j.abraham at gmail.com
> > >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 <rvanlehn at gmail.com>
> > > 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    gmx-users at gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > > >
> > > --
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> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
>
>
>
> --
> 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 <Parker.deWaal09 at kzoo.edu>
> Subject: [gmx-users] AMBER99 P450 heme topology
> To: <gmx-users at gromacs.org>
> Message-ID:
>         <
> CAJ0KcUet0qBnjB9iE5Jfjmo0qN9uRBLhDxzFOjOmuY5U6ACi7w at 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 <jernej.zidar at gmail.com>
> Subject: [gmx-users] Compiling GROMACS w CUDA 5.0 problem
> To: gmx-users at gromacs.org
> Message-ID:
>         <
> CAANrtrKjDOhsHZ_xF+CdgZy8tgvKu_TJWrEHAwxSmKksr4B+OA at 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
>
>
> ------------------------------
>
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> End of gmx-users Digest, Vol 109, Issue 153
> *******************************************
>