[gmx-users] gmx 4.5 configure options confusing

[Alan]

For gmx 4.5 beta, I see with ./configure --help:

  --without-qmmm-mopacUse modified Mopac 7 for QM-MM (see website)
  --without-qmmm-mopacUse ORCA for QM-MM

What that really means?

Thanks,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
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[gmx-users] error compiling gmx 4.5 on Mac 10.6.4

[Alan]

Hi there,

I am trying gmx 4.5 beta on Mac SL 10.6.4 with Fink, doing:

./configure CPPFLAGS="-I/sw/include" LDFLAGS="-L/sw/lib" --enable-shared
--with-gsl --with-x

and then 'make' failed with:

(cd .libs/libgmx.lax/libthread_mpi.a && ar x
/Users/alan/Downloads/gromacs-4.5-beta1/src/gmxlib/thread_mpi/.libs/libthread_mpi.a)
cc  -dynamiclib  -o .libs/libgmx.6.dylib  .libs/3dview.o .libs/atomprop.o
.libs/bondfree.o .libs/calcgrid.o .libs/calch.o .libs/chargegroup.o
.libs/checkpoint.o .libs/confio.o .libs/copyrite.o .libs/disre.o
.libs/do_fit.o .libs/enxio.o .libs/ewald_util.o .libs/ffscanf.o
.libs/filenm.o .libs/futil.o .libs/gbutil.o .libs/gmx_fatal.o
.libs/gmx_sort.o .libs/gmxcpp.o .libs/gmxfio.o .libs/ifunc.o .libs/index.o
.libs/inputrec.o .libs/cinvsqrtdata.o .libs/invblock.o .libs/macros.o
.libs/orires.o .libs/sparsematrix.o .libs/main.o .libs/maths.o .libs/matio.o
.libs/mshift.o .libs/mtop_util.o .libs/mtxio.o .libs/mvdata.o .libs/names.o
.libs/network.o .libs/nrama.o .libs/nrjac.o .libs/nrnb.o .libs/pargs.o
.libs/pbc.o .libs/pdbio.o .libs/princ.o .libs/rando.o .libs/random.o
.libs/gmx_random.o .libs/rbin.o .libs/readinp.o .libs/replace.o
.libs/rmpbc.o .libs/shift_util.o .libs/sortwater.o .libs/smalloc.o
.libs/statutil.o .libs/sfactor.o .libs/strdb.o .libs/string2.o
.libs/symtab.o .libs/topsort.o .libs/tpxio.o .libs/trnio.o .libs/trxio.o
.libs/txtdump.o .libs/typedefs.o .libs/viewit.o .libs/warninp.o .libs/wgms.o
.libs/wman.o .libs/writeps.o .libs/xdrd.o .libs/xtcio.o .libs/xvgr.o
.libs/libxdrf.o .libs/gmx_arpack.o .libs/gmx_matrix.o .libs/dihres.o
.libs/tcontrol.o .libs/splitter.o .libs/gmx_cyclecounter.o
.libs/gmx_system_xdr.o .libs/md5.o .libs/vmdio.o .libs/vmddlopen.o
.libs/sighandler.o .libs/oenv.o .libs/gmxfio_rw.o .libs/gmxfio_asc.o
.libs/gmxfio_bin.o .libs/gmxfio_xdr.o
 .libs/libgmx.lax/libnonbonded.a/nb_free_energy.o
.libs/libgmx.lax/libnonbonded.a/nb_generic.o
.libs/libgmx.lax/libnonbonded.a/nb_generic_cg.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel010.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel010_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel020.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel030.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel030_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel100.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel100_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel101.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel101_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel102.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel102_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel103.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel103_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel104.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel104_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel110.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel110_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel111.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel111_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel112.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel112_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel113.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel113_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel114.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel114_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel120.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel121.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel122.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel123.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel124.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel130.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel130_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel131.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel131_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel132.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel132_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel133.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel133_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel134.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel134_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel200.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel200_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel201.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel201_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel202.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel202_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel203.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel203_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel204.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel204_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel210.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel210_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel211.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel211_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel212.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel212_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel213.o
.libs/libgmx.lax/libnonbonded.a/nb_kernel213_x86_64_sse.o
.libs/libgmx.lax/libnonbonded.a/

Re: [gmx-users] Pullx file

[Justin A. Lemkul]

Aswathy wrote:

Dear friends,

I have pulled a ligand through the channel. Here i kept one residue at 
the mouth of the channel as reference and group1 is one of the atom in 
the side chain of the ligand.


Now I have the pullx file,( and here 1dz is the z coordinate of 
group1-group0), but here I would like to have z-coordiante of the 
ligand(instead of the single atom at the side chain)-group1. Becuase I 
beleive , that will give the correct position of the ligand (please 
correct me if I am wrong)


Is there any way to do this without running the SMD again?



Use g_traj on your trajectory.

-Justin

I have plotted the g_dist between the reference group and the ligand. 
But that does not take the place of pullx. Please give your suggestions.


Thanks,



--
Aswathy



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Pullx file

[chris . neale]

Dear Aswathy:

When you post to the list, you should include a description of what  
you eventually want to do. Here's an example of why this is important.  
If you want to make PMF then you must use the values of the pulled  
group. I'm not promoting using SMD to make PMFs, but since it is  
possible, I thought I'd point this out.


Chris.

-- original message --


Aswathy wrote:

[Hide Quoted Text]
Dear friends,

I have pulled a ligand through the channel. Here i kept one residue at
the mouth of the channel as reference and group1 is one of the atom in
the side chain of the ligand.

Now I have the pullx file,( and here 1dz is the z coordinate of
group1-group0), but here I would like to have z-coordiante of the
ligand(instead of the single atom at the side chain)-group1. Becuase I
beleive , that will give the correct position of the ligand (please
correct me if I am wrong)

Is there any way to do this without running the SMD again?
Use g_traj on your trajectory.

-Justin

[Hide Quoted Text]
I have plotted the g_dist between the reference group and the ligand.
But that does not take the place of pullx. Please give your suggestions.

Thanks,



--
Aswathy

--
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[gmx-users] Re: error compiling gmx 4.5 on Mac 10.6.4

[Alan]

To myself.

Removing --enable-shared and compilation went fine.

Alan

On Sat, Jul 31, 2010 at 11:41, Alan  wrote:

> Hi there,
>
> I am trying gmx 4.5 beta on Mac SL 10.6.4 with Fink, doing:
>
> ./configure CPPFLAGS="-I/sw/include" LDFLAGS="-L/sw/lib" --enable-shared
> --with-gsl --with-x
>
> and then 'make' failed with:
>
> (cd .libs/libgmx.lax/libthread_mpi.a && ar x
> /Users/alan/Downloads/gromacs-4.5-beta1/src/gmxlib/thread_mpi/.libs/libthread_mpi.a)
> cc  -dynamiclib  -o .libs/libgmx.6.dylib  .libs/3dview.o .libs/atomprop.o
> .libs/bondfree.o .libs/calcgrid.o .libs/calch.o .libs/chargegroup.o
> .libs/checkpoint.o .libs/confio.o .libs/copyrite.o .libs/disre.o
> .libs/do_fit.o .libs/enxio.o .libs/ewald_util.o .libs/ffscanf.o
> .libs/filenm.o .libs/futil.o .libs/gbutil.o .libs/gmx_fatal.o
> .libs/gmx_sort.o .libs/gmxcpp.o .libs/gmxfio.o .libs/ifunc.o .libs/index.o
> .libs/inputrec.o .libs/cinvsqrtdata.o .libs/invblock.o .libs/macros.o
> .libs/orires.o .libs/sparsematrix.o .libs/main.o .libs/maths.o .libs/matio.o
> .libs/mshift.o .libs/mtop_util.o .libs/mtxio.o .libs/mvdata.o .libs/names.o
> .libs/network.o .libs/nrama.o .libs/nrjac.o .libs/nrnb.o .libs/pargs.o
> .libs/pbc.o .libs/pdbio.o .libs/princ.o .libs/rando.o .libs/random.o
> .libs/gmx_random.o .libs/rbin.o .libs/readinp.o .libs/replace.o
> .libs/rmpbc.o .libs/shift_util.o .libs/sortwater.o .libs/smalloc.o
> .libs/statutil.o .libs/sfactor.o .libs/strdb.o .libs/string2.o
> .libs/symtab.o .libs/topsort.o .libs/tpxio.o .libs/trnio.o .libs/trxio.o
> .libs/txtdump.o .libs/typedefs.o .libs/viewit.o .libs/warninp.o .libs/wgms.o
> .libs/wman.o .libs/writeps.o .libs/xdrd.o .libs/xtcio.o .libs/xvgr.o
> .libs/libxdrf.o .libs/gmx_arpack.o .libs/gmx_matrix.o .libs/dihres.o
> .libs/tcontrol.o .libs/splitter.o .libs/gmx_cyclecounter.o
> .libs/gmx_system_xdr.o .libs/md5.o .libs/vmdio.o .libs/vmddlopen.o
> .libs/sighandler.o .libs/oenv.o .libs/gmxfio_rw.o .libs/gmxfio_asc.o
> .libs/gmxfio_bin.o .libs/gmxfio_xdr.o
>  .libs/libgmx.lax/libnonbonded.a/nb_free_energy.o
> .libs/libgmx.lax/libnonbonded.a/nb_generic.o
> .libs/libgmx.lax/libnonbonded.a/nb_generic_cg.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel010.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel010_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel020.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel030.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel030_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel100.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel100_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel101.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel101_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel102.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel102_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel103.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel103_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel104.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel104_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel110.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel110_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel111.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel111_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel112.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel112_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel113.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel113_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel114.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel114_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel120.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel121.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel122.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel123.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel124.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel130.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel130_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel131.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel131_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel132.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel132_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel133.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel133_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel134.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel134_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel200.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel200_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel201.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel201_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel202.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel202_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel203.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel203_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel204.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel204_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel210.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel210_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel211.o
> .libs/li

[gmx-users] tests for gmx 4.5

[Alan]

Is there a proper set of tests for gmx 4.5 because neither
ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz or "git clone git://
git.gromacs.org/regressiontests.git" is working due to the several
modifications done in gmx 4.5 including automatic thread for mdrun (I am
using a Mac with dual core) and more warnings.

Thanks,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] gmx 4.5 issue with grompp

[Alan]

I am trying this test of mine:


wget -c "
http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1BVG";
-O 1BVG.pdb
grep 'ATOM  ' 1BVG.pdb>| Protein.pdb

pdb2gmx -ff amber99sb -f Protein.pdb -o Protein2.pdb -p Protein.top -water
spce -ignh

editconf -bt triclinic -f Protein2.pdb -o Protein3.pdb -d 1.0

genbox -cp Protein3.pdb -o Protein_b4ion.pdb -p Protein.top -cs

cat << EOF >| em.mdp
define   = -DFLEXIBLE
integrator   = cg ; steep
nsteps   = 200
constraints  = none
emtol= 1000.0
nstcgsteep   = 10 ; do a steep every 10 steps of cg
emstep   = 0.01 ; used with steep
nstcomm  = 1
coulombtype  = PME
ns_type  = grid
rlist= 1.0
rcoulomb = 1.0
rvdw = 1.4
Tcoupl   = no
Pcoupl   = no
gen_vel  = no
nstxout  = 0 ; write coords every # step
optimize_fft = yes
EOF

cat << EOF >| md.mdp
integrator   = md
nsteps   = 1000
dt   = 0.002
constraints  = all-bonds
nstcomm  = 1
ns_type  = grid
rlist= 1.2
rcoulomb = 1.1
rvdw = 1.0
vdwtype  = shift
rvdw-switch  = 0.9
coulombtype  = PME-Switch
Tcoupl   = v-rescale
tau_t= 0.1 0.1
tc-grps  = protein non-protein
ref_t= 300 300
Pcoupl   = parrinello-rahman
Pcoupltype   = isotropic
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
gen_vel  = yes
nstxout  = 2 ; write coords every # step
lincs-iter   = 2
DispCorr = EnerPres
optimize_fft = yes
EOF

grompp -f em.mdp -c Protein_b4ion.pdb -p Protein.top -o Protein_b4ion.tpr
\cp Protein.top Protein_ion.top

echo 13 | genion -s Protein_b4ion.tpr -o Protein_b4em.pdb -neutral -conc
0.15 -p Protein_ion.top -norandom

\mv Protein_ion.top Protein.top

grompp -f em.mdp -c Protein_b4em.pdb -p Protein.top -o em.tpr

mdrun -v -deffnm em

grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr

And it fails for the command above with:

---
Program grompp, VERSION 4.5-beta1
Source code file: inputrec.c, line: 161

Software inconsistency error:
Unknown epc value


Any ideas? Thanks,

Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] GROMACS-4.5-beta1 is out!

[Amit Choubey]

Hi Rossen,

Could you send me a documentation of memory usage by gromacs-4.5-beta1. I
would like to know the maximum no. of atoms that we can simulate on our
university supercomputer.

amit

On Fri, Jul 30, 2010 at 12:20 PM, Rossen Apostolov <
rossen.aposto...@cbr.su.se> wrote:

>
> After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is
> out!
>
> It is full of many new and exciting features, please try them out!
>
> If something is not working as expected, please send a mail or file a
> bugzilla report.
>
> For developers: there is a new branch for stable releases called
> "release-4-5-patches". Bugfixes should be applied there **first**, and if
> needed, merged from that branch into the master after the fix. See
> http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for more
> information.
>
>
> New features:
>
>- 2D decomposition support for PME: improved load balancing with up to
>40% overall performance improvement for large systems.
>- Memory usage is improved for very large systems, allowing simulations
>of >100 million atoms.
>- Running on multi-core nodes now automatically uses threads for domain
>decomposition through the built-in threaded MPI library
>- GPU computing support
>- Check-pointing is made more secure:MD5sum are used to verify that all
>files are correctly in-place before a simulation is appended. Output file
>appending at continuation is turned on by default
>- Full Cmake support. Autoconf/automake will be deprecated after the
>final 4.5 release!
>- Full support for 7 AMBER force fields
>- Support for CHARMM27, including cmap for dihedrals
>- Efficient Generalized-Born implicit solvent support including the
>Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating
>the generalized Born-interaction formula for greater speed, and optimized
>SSE-routines for both cut-off and all-vs-all simulations.
>- Support for nucleic acid simulations
>- Support for Velocity-Verlet integrators for reversible T- and
>P-coupling; MTTK pressure control integrators; Nose-Hoover chains
>- Support for Bennett acceptance ratio (BAR) free energy calculations
>- Decoupling group setup for free energy
>- File formats: All GROMACS tools can now read any VMD supported
>trajectory format, without converting trajectory first. (VMD is required)
>- g_rdf was a little bit enhanced that structure factors can be
>calculated for any system, by supplying the necessary data via sfactor.dat.
>Most of the common atomtypes are already contained, but everybody who needs
>more freedom can enhance the table
>- Library support for "dynamic index groups" based on textual
>selections (experimental feature). See the tool g_select, the included
>template.c, or Doxygen documentation for information on how to write
>analysis tools using the library. Existing tools have not (yet) been
>converted.
>- g_tune_pme: For a given number of processes or threads this tool
>systematically times mdrun with various numbers of PME-only nodes and
>determines which setting is fastest. It also checks whether performance can
>be enhanced by shifting load between the real and the reciprocal space part
>of the Ewald sum.
>- g_membed: a very convenient utility for embedding membrane proteins
>into equilibrated lipid bilayers
>
>
> Big thanks to all developers, contributors and users!
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] GROMACS-4.5-beta1 is out!

[David van der Spoel]

On 2010-07-31 21.34, Amit Choubey wrote:

Hi Rossen,

Could you send me a documentation of memory usage by gromacs-4.5-beta1.
I would like to know the maximum no. of atoms that we can simulate on
our university supercomputer.


It is roughly linear with the number of atoms. Just try it.


amit

On Fri, Jul 30, 2010 at 12:20 PM, Rossen Apostolov
mailto:rossen.aposto...@cbr.su.se>> wrote:


After months of hard work and 2449 patches, the new
gromacs-4.5-beta1 is out!

It is full of many new and exciting features, please try them out!

If something is not working as expected, please send a mail or file
a bugzilla report.

For developers: there is a new branch for stable releases called
"release-4-5-patches". Bugfixes should be applied there **first**,
and if needed, merged from that branch into the master after the
fix. See
http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for
more information.


New features:

* 2D decomposition support for PME: improved load balancing with
  up to 40% overall performance improvement for large systems.
* Memory usage is improved for very large systems, allowing
  simulations of >100 million atoms.
* Running on multi-core nodes now automatically uses threads for
  domain decomposition through the built-in threaded MPI library
* GPU computing support
* Check-pointing is made more secure:MD5sum are used to verify
  that all files are correctly in-place before a simulation is
  appended. Output file appending at continuation is turned on
  by default
* Full Cmake support. Autoconf/automake will be deprecated after
  the final 4.5 release!
* Full support for 7 AMBER force fields
* Support for CHARMM27, including cmap for dihedrals
* Efficient Generalized-Born implicit solvent support including
  the Still/HCT/OBC-models to compute the Born radii, a novel
  way of tabulating the generalized Born-interaction formula for
  greater speed, and optimized SSE-routines for both cut-off and
  all-vs-all simulations.
* Support for nucleic acid simulations
* Support for Velocity-Verlet integrators for reversible T- and
  P-coupling; MTTK pressure control integrators; Nose-Hoover chains
* Support for Bennett acceptance ratio (BAR) free energy
  calculations
* Decoupling group setup for free energy
* File formats: All GROMACS tools can now read any VMD supported
  trajectory format, without converting trajectory first. (VMD
  is required)
* g_rdf was a little bit enhanced that structure factors can be
  calculated for any system, by supplying the necessary data via
  sfactor.dat. Most of the common atomtypes are already
  contained, but everybody who needs more freedom can enhance
  the table
* Library support for "dynamic index groups" based on textual
  selections (experimental feature). See the tool g_select, the
  included template.c, or Doxygen documentation for information
  on how to write analysis tools using the library. Existing
  tools have not (yet) been converted.
* g_tune_pme: For a given number of processes or threads this
  tool systematically times mdrun with various numbers of
  PME-only nodes and determines which setting is fastest. It
  also checks whether performance can be enhanced by shifting
  load between the real and the reciprocal space part of the
  Ewald sum.
* g_membed: a very convenient utility for embedding membrane
  proteins into equilibrated lipid bilayers


Big thanks to all developers, contributors and users!

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Re: [gmx-users] GROMACS-4.5-beta1 is out!

[ms]

As a young GROMACS user, thank you a lot! I just want to ask:

On 30/07/10 20:20, Rossen Apostolov wrote:

* Efficient Generalized-Born implicit solvent support including the
Still/HCT/OBC-models to compute the Born radii, a novel way of
tabulating the generalized Born-interaction formula for greater
speed, and optimized SSE-routines for both cut-off and all-vs-all
simulations.


- Is there a 4.5 version of the manual which documents the implicit 
solvent feature?
- It is already tested enough that one can be comfortable (albeit 
cautious) using it for real work, or does it require a lot of testing, 
in your opinion?


thanks again!

m.
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[gmx-users] grompp error-box vectors

[Moeed]

Dear gmx users,

I am trying to compress a single polymer chain. grompp is giving the error
below:

Program mdrun, VERSION 4.0.7
Source code file: ns.c, line: 2299

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.

I dont realize the error exactly...I tried compressing with different ref
pressures of 30 10 and 1 bar.. can you please guideme whre the problem lies.


Actually later I will have to work with much longer chains so this
compressing issue can become even more challanging. I wanted to know how I
can decide on P coupling parameters (tau_P, pcoupling type or even coupling
algorithm ..) when it comes to compressing different chain lengths and
different number of chains in the box...

Thank you,


pbc  =  xyz   ; use priodic BCs in all
directions

;Run control
integrator  =  md ; type of dynamics algorithm. Here
md uses a leap-frog algorithm for integrating Newtons's eq of motion
dt  =  0.001 ; in ps !
nsteps  =  400  ; length of simulation=
nsteps*dt
nstcomm =  1 ; frequency for center of mass
motion removal

;Output control
nstenergy   =  100  ; frequency to write energies to
energy file. i.e., energies and other statistical data are stored every 10
steps
nstxout =  100 ; frequency to write
coordinates/velocity/force to output trajectory file. how often snapshots
are collected= nstxout*dt
nstvout =  0
nstfout =  0
nstlog  =  1000 ; frequency to write energies to
log file
nstxtcout  =  0 ; frequency to write coordinates to
xtc trajectory

;Neighbor searching
nstlist =  10 ; frequency to update neighbor
list. Neighborlist will be updated at least every 10 steps. Manual p80
ns_type =  grid ; make a grid in the box and
only check atoms in neighboring grid cells when constructing a new neighbor
list every nstlist steps

;Electrostatics/VdW
;coulombtype =  PME  ; tells gromacs how to
model electrostatics. Shift: Coulomb/LJ potential is decreased over the
whole range and forces decay smoothly to zero between
vdw-type=  Shift   ; rcoulomb-switch/rvw-switch &
rcoulomb/rvdw
rcoulomb-switch =  0; where to start switching the
Coulomb potential
rvdw-switch =  0.9 ;0 ; where to start switching the
LJ potential

;Cut-offs
rlist   =  1.1 ; in nm. Cut-off distance for
short-range neighbor list
rcoulomb=  1.1 ;1.0 ; distance for coulomb cut-off
rvdw=  1.0 ; distance for coulomb cut-off

;Temperature coupling
Tcoupl  =  v-rescale;berendsen
tc-grps =  System  ;HEX   ; groups to couple to
thermostat; Berendsen temperature coupling is on in these groups
tau_t   =  0.1 ;0.1   ; time constant for T
coupling
ref_t   =  300 ;300   ; reference T for
coupling. When you alter the T, don't forget to change the gen_temp for
velocity generation

;Pressure coupling
Pcoupl  =  Parrinello-Rahman;berendsen
Pcoupltype  =  semiisotropic;isotropic ; isotropic: means the
box expands and contracts in all directions(x,y,z)in order to maintain the
proper pressure;semiisotropic: isotropic in x & y directions
tau_p   =  1  1   ;0.5   ; time constant for
coupling in ps
compressibility =  4.5e-5 4.5e-5   ; compressibility of solvent
used in simulation in 1/bar
ref_p   =  1.01.0   ; reference P for coupling
in bar

;Velocity generation   Generate velocites is on at 300
K. Manual p155
gen_vel =  yes ; generate velocites according to
Maxwell distribution at T: gen_temp with random gen seed gen_seed
gen_temp=  300.0 ; T for Maxwell distribution
gen_seed=  173529 ; used to initialize random
generator for random velocities

;Bonds
constraints =  none ;all-bonds   ; sets the LINCS constraint
for all bonds
constraint-algorithm = lincs
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Re: [gmx-users] grompp error-box vectors

[Justin A. Lemkul]

Moeed wrote:

Dear gmx users,

I am trying to compress a single polymer chain. grompp is giving the 
error below:


Program mdrun, VERSION 4.0.7
Source code file: ns.c, line: 2299

Fatal error:
One of the box vectors has become shorter than twice the cut-off length 
or box_yy-|box_zy| or box_zz has become smaller than the cut-off.


I dont realize the error exactly...I tried compressing with different 
ref pressures of 30 10 and 1 bar.. can you please guideme whre the 
problem lies.




Your box is compressing too fast and you're violating the minimum image 
convention:

http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

I suspect you'll have to compress your system more slowly, otherwise your box 
vectors are just going to crash in on your polymer chain before it has time to 
adjust its configuration.


-Justin

Actually later I will have to work with much longer chains so this 
compressing issue can become even more challanging. I wanted to know how 
I can decide on P coupling parameters (tau_P, pcoupling type or even 
coupling algorithm ..) when it comes to compressing different chain 
lengths and different number of chains in the box...


Thank you,


pbc  =  xyz   ; use priodic BCs in all 
directions
   
;Run control
integrator  =  md ; type of dynamics algorithm. 
Here md uses a leap-frog algorithm for integrating Newtons's eq of motion

dt  =  0.001 ; in ps !
nsteps  =  400  ; length of simulation= 
nsteps*dt 
nstcomm =  1 ; frequency for center of mass 
motion removal   


;Output control
nstenergy   =  100  ; frequency to write 
energies to energy file. i.e., energies and other statistical data are 
stored every 10 steps
nstxout =  100 ; frequency to write 
coordinates/velocity/force to output trajectory file. how often 
snapshots are collected= nstxout*dt

nstvout =  0
nstfout =  0
nstlog  =  1000 ; frequency to write 
energies to log file
nstxtcout  =  0 ; frequency to write coordinates 
to xtc trajectory


;Neighbor searching
nstlist =  10 ; frequency to update neighbor 
list. Neighborlist will be updated at least every 10 steps. Manual p80
ns_type =  grid ; make a grid in the box and 
only check atoms in neighboring grid cells when constructing a new 
neighbor list every nstlist steps


;Electrostatics/VdW
;coulombtype =  PME  ; tells gromacs how to 
model electrostatics. Shift: Coulomb/LJ potential is decreased over the 
whole range and forces decay smoothly to zero between 
vdw-type=  Shift   ; rcoulomb-switch/rvw-switch 
& rcoulomb/rvdw
rcoulomb-switch =  0; where to start switching 
the Coulomb potential
rvdw-switch =  0.9 ;0 ; where to start switching 
the LJ potential   


;Cut-offs
rlist   =  1.1 ; in nm. Cut-off distance for 
short-range neighbor list

rcoulomb=  1.1 ;1.0 ; distance for coulomb cut-off
rvdw=  1.0 ; distance for coulomb cut-off

;Temperature coupling   
Tcoupl  =  v-rescale;berendsen
tc-grps =  System  ;HEX   ; groups to couple to 
thermostat; Berendsen temperature coupling is on in these groups   
tau_t   =  0.1 ;0.1   ; time constant for T 
coupling
ref_t   =  300 ;300   ; reference T for 
coupling. When you alter the T, don't forget to change the gen_temp for 
velocity generation


;Pressure coupling
Pcoupl  =  Parrinello-Rahman;berendsen
Pcoupltype  =  semiisotropic;isotropic ; isotropic: means 
the box expands and contracts in all directions(x,y,z)in order to 
maintain the proper pressure;semiisotropic: isotropic in x & y directions
tau_p   =  1  1   ;0.5   ; time constant for 
coupling in ps   
compressibility =  4.5e-5 4.5e-5   ; compressibility of 
solvent used in simulation in 1/bar
ref_p   =  1.01.0   ; reference P for 
coupling in bar


;Velocity generation   Generate velocites is on at 
300 K. Manual p155
gen_vel =  yes ; generate velocites 
according to Maxwell distribution at T: gen_temp with random gen seed 
gen_seed

gen_temp=  300.0 ; T for Maxwell distribution
gen_seed=  173529 ; used to initialize 
random generator for random velocities


;Bonds
constraints =  none ;all-bonds   ; sets the LINCS 
constraint 

Re: [gmx-users] Install error for gmx-4.5_beta1

[Roland Schulz]

Hi,

in general running in parallel (-j) doesn't help for install. I suggest to
use -j only for "make" and not for "make install"

Roland

On Fri, Jul 30, 2010 at 3:38 PM, Justin A. Lemkul  wrote:

>
> Hi,
>
> Thanks to the developers for the release of the 4.5 beta.  Unfortunately,
> I'm having a minor issue getting it to install.  My system is Mac OSX 10.5.8
> (Intel), gcc 4.0.1, fftw 3.0.1.  Installation procedure:
>
> $ ./configure --prefix=/usr/local/gmx_4.5_beta1 --with-gsl
> CPPFLAGS="-I/usr/local/fftw/include -I/sw/include"
> LDFLAGS="-L/usr/local/fftw/lib -L/sw/lib"
>
> $ make -j 2
>
> $ sudo make -j 2 install
>
> Error message:
>
> Making install in gmxdemo
> make[4]: Nothing to be done for `install-exec-am'.
> test -z "/usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo" ||
> ../../../config/install-sh -c -d
> "/usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo"
> test -z "/usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo" ||
> ../../../config/install-sh -c -d
> "/usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo"
> mkdir: /usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo: File exists
> make[4]: *** [install-gmxdemoSCRIPTS] Error 1
> make[4]: *** Waiting for unfinished jobs
>  /usr/bin/install -c -m 644 cpeptide.pdb
> '/usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo'
> make[3]: *** [install-am] Error 2
> make[2]: *** [install-recursive] Error 1
> make[1]: *** [install-recursive] Error 1
> make: *** [install-recursive] Error 1
>
>
> The funny part is that if I re-issue the exact same make install command as
> above, the process completes.  Is the issue related to the duplicate "test
> -z" lines shown above?
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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
>



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865-241-1537, ORNL PO BOX 2008 MS6309
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Re: [gmx-users] Another install error: gmx-4.5 beta1

[Roland Schulz]

Hi,

look at /usr/include/regex.h line 68. What is/are the keyword before. I
assume this is (re)defined in some of the GROMACS or system include files
and thus breaks the regex.h. You can run the cc command line shown below
with all the options from the shown folder and add -E to the command-line.
This shows you were this is defined. If you can't find it send me the output
of cc -E and the regex.h as PM attachment.

Roland

On Fri, Jul 30, 2010 at 5:53 PM, Justin A. Lemkul  wrote:

>
> Hi,
>
> I'm trying to install the newest beta on our university's supercomputer,
> but I'm encountering an error during compilation.  It's an aging system, so
> this might be somewhat difficult to solve.  Here are the specs:
>
> Mac OSX 10.3
> 2.3 GHz PowerPC 970FX processors
> gcc 3.3
> fftw 3.0.1
>
> Configuration went without a hitch, with config.log indicating all
> necessary headers, libraries, etc. were found.
>
> ./configure --prefix=/home/rdiv1001/gromacs-4.5_beta1
> CPPFLAGS="-I/home/rdiv1001/fftw-3.0.1/include"
> LDFLAGS="-L/home/rdiv1001/fftw-3.0.1/lib" --program-suffix=_4.5_beta1
> --disable-threads
>
> Compilation fails with the following:
>
> Making all in selection
> ...
> /bin/sh ../../../libtool --tag=CC   --mode=compile cc -DHAVE_CONFIG_H -I.
> -I../../../src -I/usr/include/libxml2 -I../../../include
> -I/home/rdiv1001/fftw-3.0.1/include  -O3 -fomit-frame-pointer
> -finline-functions -Wall -Wno-unused -faltivec -funroll-all-loops -std=gnu99
> -mcpu=7450 -mtune=970 -MT sm_keywords.lo -MD -MP -MF .deps/sm_keywords.Tpo
> -c -o sm_keywords.lo sm_keywords.c
>  cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2
> -I../../../include -I/home/rdiv1001/fftw-3.0.1/include -O3
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -faltivec
> -funroll-all-loops -std=gnu99 -mcpu=7450 -mtune=970 -MT sm_keywords.lo -MD
> -MP -MF .deps/sm_keywords.Tpo -c sm_keywords.c -o sm_keywords.o
> In file included from sm_keywords.c:41:
> /usr/include/regex.h:68: error: parse error before "regoff_t"
> /usr/include/regex.h:78: error: parse error before "regoff_t"
> /usr/include/regex.h:124: error: parse error before "regmatch_t"
> make[4]: *** [sm_keywords.lo] Error 1
> make[3]: *** [all-recursive] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all] Error 2
> make: *** [all-recursive] Error 1
>
> Any ideas for a fix?
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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
>



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865-241-1537, ORNL PO BOX 2008 MS6309
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Re: [gmx-users] Install error for gmx-4.5_beta1

[Justin A. Lemkul]

Roland Schulz wrote:

Hi,

in general running in parallel (-j) doesn't help for install. I suggest 
to use -j only for "make" and not for "make install"




Ah, foolish of me.  I got carried away with my copy and paste.  Thanks.

-Justin


Roland

On Fri, Jul 30, 2010 at 3:38 PM, Justin A. Lemkul > wrote:



Hi,

Thanks to the developers for the release of the 4.5 beta.
 Unfortunately, I'm having a minor issue getting it to install.  My
system is Mac OSX 10.5.8 (Intel), gcc 4.0.1, fftw 3.0.1.
 Installation procedure:

$ ./configure --prefix=/usr/local/gmx_4.5_beta1 --with-gsl
CPPFLAGS="-I/usr/local/fftw/include -I/sw/include"
LDFLAGS="-L/usr/local/fftw/lib -L/sw/lib"

$ make -j 2

$ sudo make -j 2 install

Error message:

Making install in gmxdemo
make[4]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo" ||
../../../config/install-sh -c -d
"/usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo"
test -z "/usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo" ||
../../../config/install-sh -c -d
"/usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo"
mkdir: /usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo: File exists
make[4]: *** [install-gmxdemoSCRIPTS] Error 1
make[4]: *** Waiting for unfinished jobs
 /usr/bin/install -c -m 644 cpeptide.pdb
'/usr/local/gmx_4.5_beta1/share/gromacs/tutor/gmxdemo'
make[3]: *** [install-am] Error 2
make[2]: *** [install-recursive] Error 1
make[1]: *** [install-recursive] Error 1
make: *** [install-recursive] Error 1


The funny part is that if I re-issue the exact same make install
command as above, the process completes.  Is the issue related to
the duplicate "test -z" lines shown above?

-Justin

-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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865-241-1537, ORNL PO BOX 2008 MS6309


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Another install error: gmx-4.5 beta1

[Justin A. Lemkul]

Roland Schulz wrote:

Hi,

look at /usr/include/regex.h line 68. What is/are the keyword before. I 


Line 68 occurs very early in the file, and corresponds to:

typedef off_t regoff_t;

In regex.h, there are 60 lines of comments followed by:

#ifndef _REGEX_H_
#define _REGEX_H_

#include 

/* types */
typedef off_t regoff_t;

assume this is (re)defined in some of the GROMACS or system include 
files and thus breaks the regex.h. You can run the cc command line shown 
below with all the options from the shown folder and add -E to the 
command-line. This shows you were this is defined. If you can't find it 
send me the output of cc -E and the regex.h as PM attachment.




Adding -E to the cc command doesn't produce anything.  Perhaps I've done 
something wrong, but if I understood you, the command should be:


cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2 -I../../../include 
-I/home/rdiv1001/fftw-3.0.1/include -O3 -fomit-frame-pointer -finline-functions 
-Wall -Wno-unused -faltivec -funroll-all-loops -std=gnu99 -mcpu=7450 -mtune=970 
-MT sm_keywords.lo -MD -MP -MF .deps/sm_keywords.Tpo -c sm_keywords.c -o 
sm_keywords.o -E


I'll send you the regex.h file off-list.  Thanks for your attention.

-Justin


Roland

On Fri, Jul 30, 2010 at 5:53 PM, Justin A. Lemkul > wrote:



Hi,

I'm trying to install the newest beta on our university's
supercomputer, but I'm encountering an error during compilation.
 It's an aging system, so this might be somewhat difficult to solve.
 Here are the specs:

Mac OSX 10.3
2.3 GHz PowerPC 970FX processors
gcc 3.3
fftw 3.0.1

Configuration went without a hitch, with config.log indicating all
necessary headers, libraries, etc. were found.

./configure --prefix=/home/rdiv1001/gromacs-4.5_beta1
CPPFLAGS="-I/home/rdiv1001/fftw-3.0.1/include"
LDFLAGS="-L/home/rdiv1001/fftw-3.0.1/lib"
--program-suffix=_4.5_beta1 --disable-threads

Compilation fails with the following:

Making all in selection
...
/bin/sh ../../../libtool --tag=CC   --mode=compile cc
-DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2
-I../../../include -I/home/rdiv1001/fftw-3.0.1/include  -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -faltivec
-funroll-all-loops -std=gnu99 -mcpu=7450 -mtune=970 -MT
sm_keywords.lo -MD -MP -MF .deps/sm_keywords.Tpo -c -o
sm_keywords.lo sm_keywords.c
 cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2
-I../../../include -I/home/rdiv1001/fftw-3.0.1/include -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -faltivec
-funroll-all-loops -std=gnu99 -mcpu=7450 -mtune=970 -MT
sm_keywords.lo -MD -MP -MF .deps/sm_keywords.Tpo -c sm_keywords.c -o
sm_keywords.o
In file included from sm_keywords.c:41:
/usr/include/regex.h:68: error: parse error before "regoff_t"
/usr/include/regex.h:78: error: parse error before "regoff_t"
/usr/include/regex.h:124: error: parse error before "regmatch_t"
make[4]: *** [sm_keywords.lo] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1

Any ideas for a fix?

-Justin

-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- 
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Please search the archive at http://www.gromacs.org/search before
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--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 
865-241-1537, ORNL PO BOX 2008 MS6309


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] Another install error: gmx-4.5 beta1

[Roland Schulz]

Hi Justin,

try to add "#include " before the include of regex.h in
sm-keywords.c.

Roland

On Sun, Aug 1, 2010 at 12:49 AM, Justin A. Lemkul  wrote:

>
>
> Roland Schulz wrote:
>
>> Hi,
>>
>> look at /usr/include/regex.h line 68. What is/are the keyword before. I
>>
>
> Line 68 occurs very early in the file, and corresponds to:
>
> typedef off_t regoff_t;
>
> In regex.h, there are 60 lines of comments followed by:
>
> #ifndef _REGEX_H_
> #define _REGEX_H_
>
> #include 
>
> /* types */
> typedef off_t regoff_t;
>
>
>  assume this is (re)defined in some of the GROMACS or system include files
>> and thus breaks the regex.h. You can run the cc command line shown below
>> with all the options from the shown folder and add -E to the command-line.
>> This shows you were this is defined. If you can't find it send me the output
>> of cc -E and the regex.h as PM attachment.
>>
>>
> Adding -E to the cc command doesn't produce anything.  Perhaps I've done
> something wrong, but if I understood you, the command should be:
>
> cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2
> -I../../../include -I/home/rdiv1001/fftw-3.0.1/include -O3
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -faltivec
> -funroll-all-loops -std=gnu99 -mcpu=7450 -mtune=970 -MT sm_keywords.lo -MD
> -MP -MF .deps/sm_keywords.Tpo -c sm_keywords.c -o sm_keywords.o -E
>
> I'll send you the regex.h file off-list.  Thanks for your attention.
>
> -Justin
>
>  Roland
>>
>>
>> On Fri, Jul 30, 2010 at 5:53 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>Hi,
>>
>>I'm trying to install the newest beta on our university's
>>supercomputer, but I'm encountering an error during compilation.
>> It's an aging system, so this might be somewhat difficult to solve.
>> Here are the specs:
>>
>>Mac OSX 10.3
>>2.3 GHz PowerPC 970FX processors
>>gcc 3.3
>>fftw 3.0.1
>>
>>Configuration went without a hitch, with config.log indicating all
>>necessary headers, libraries, etc. were found.
>>
>>./configure --prefix=/home/rdiv1001/gromacs-4.5_beta1
>>CPPFLAGS="-I/home/rdiv1001/fftw-3.0.1/include"
>>LDFLAGS="-L/home/rdiv1001/fftw-3.0.1/lib"
>>--program-suffix=_4.5_beta1 --disable-threads
>>
>>Compilation fails with the following:
>>
>>Making all in selection
>>...
>>/bin/sh ../../../libtool --tag=CC   --mode=compile cc
>>-DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2
>>-I../../../include -I/home/rdiv1001/fftw-3.0.1/include  -O3
>>-fomit-frame-pointer -finline-functions -Wall -Wno-unused -faltivec
>>-funroll-all-loops -std=gnu99 -mcpu=7450 -mtune=970 -MT
>>sm_keywords.lo -MD -MP -MF .deps/sm_keywords.Tpo -c -o
>>sm_keywords.lo sm_keywords.c
>> cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2
>>-I../../../include -I/home/rdiv1001/fftw-3.0.1/include -O3
>>-fomit-frame-pointer -finline-functions -Wall -Wno-unused -faltivec
>>-funroll-all-loops -std=gnu99 -mcpu=7450 -mtune=970 -MT
>>sm_keywords.lo -MD -MP -MF .deps/sm_keywords.Tpo -c sm_keywords.c -o
>>sm_keywords.o
>>In file included from sm_keywords.c:41:
>>/usr/include/regex.h:68: error: parse error before "regoff_t"
>>/usr/include/regex.h:78: error: parse error before "regoff_t"
>>/usr/include/regex.h:124: error: parse error before "regmatch_t"
>>make[4]: *** [sm_keywords.lo] Error 1
>>make[3]: *** [all-recursive] Error 1
>>make[2]: *** [all-recursive] Error 1
>>make[1]: *** [all] Error 2
>>make: *** [all-recursive] Error 1
>>
>>Any ideas for a fix?
>>
>>-Justin
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/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
>>
>>
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > >
>>
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> =

Re: [gmx-users] gmx 4.5 issue with grompp

[Roland Schulz]

Alan,

with the following change your example works for me.

diff --git a/src/gmxlib/inputrec.c b/src/gmxlib/inputrec.c
index 581ae4c..e148612 100644
--- a/src/gmxlib/inputrec.c
+++ b/src/gmxlib/inputrec.c
@@ -169,7 +169,7 @@ int ir_optimal_nstpcouple(const t_inputrec *ir)
 {
 int  nmin,nwanted,n;

-nmin = pcouple_min_integration_steps(ir->etc);
+nmin = pcouple_min_integration_steps(ir->epc);

 nwanted = nst_wanted(ir);

Or you can also update from git.

@Berk: Could you please verify that this fix is correct?

Roland

On Sat, Jul 31, 2010 at 2:22 PM, Alan  wrote:

> I am trying this test of mine:
>
>
> wget -c "
> http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1BVG";
> -O 1BVG.pdb
> grep 'ATOM  ' 1BVG.pdb>| Protein.pdb
>
> pdb2gmx -ff amber99sb -f Protein.pdb -o Protein2.pdb -p Protein.top -water
> spce -ignh
>
> editconf -bt triclinic -f Protein2.pdb -o Protein3.pdb -d 1.0
>
> genbox -cp Protein3.pdb -o Protein_b4ion.pdb -p Protein.top -cs
>
> cat << EOF >| em.mdp
> define   = -DFLEXIBLE
> integrator   = cg ; steep
> nsteps   = 200
> constraints  = none
> emtol= 1000.0
> nstcgsteep   = 10 ; do a steep every 10 steps of cg
> emstep   = 0.01 ; used with steep
> nstcomm  = 1
> coulombtype  = PME
> ns_type  = grid
> rlist= 1.0
> rcoulomb = 1.0
> rvdw = 1.4
> Tcoupl   = no
> Pcoupl   = no
> gen_vel  = no
> nstxout  = 0 ; write coords every # step
> optimize_fft = yes
> EOF
>
> cat << EOF >| md.mdp
> integrator   = md
> nsteps   = 1000
> dt   = 0.002
> constraints  = all-bonds
> nstcomm  = 1
> ns_type  = grid
> rlist= 1.2
> rcoulomb = 1.1
> rvdw = 1.0
> vdwtype  = shift
> rvdw-switch  = 0.9
> coulombtype  = PME-Switch
> Tcoupl   = v-rescale
> tau_t= 0.1 0.1
> tc-grps  = protein non-protein
> ref_t= 300 300
> Pcoupl   = parrinello-rahman
> Pcoupltype   = isotropic
> tau_p= 0.5
> compressibility  = 4.5e-5
> ref_p= 1.0
> gen_vel  = yes
> nstxout  = 2 ; write coords every # step
> lincs-iter   = 2
> DispCorr = EnerPres
> optimize_fft = yes
> EOF
>
> grompp -f em.mdp -c Protein_b4ion.pdb -p Protein.top -o Protein_b4ion.tpr
> \cp Protein.top Protein_ion.top
>
> echo 13 | genion -s Protein_b4ion.tpr -o Protein_b4em.pdb -neutral -conc
> 0.15 -p Protein_ion.top -norandom
>
> \mv Protein_ion.top Protein.top
>
> grompp -f em.mdp -c Protein_b4em.pdb -p Protein.top -o em.tpr
>
> mdrun -v -deffnm em
>
> grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr
>
> And it fails for the command above with:
>
> ---
> Program grompp, VERSION 4.5-beta1
> Source code file: inputrec.c, line: 161
>
> Software inconsistency error:
> Unknown epc value
>
>
> Any ideas? Thanks,
>
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
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865-241-1537, ORNL PO BOX 2008 MS6309
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