Re: [gmx-users] mdrun_mpi error

[aiswarya pawar]

i used the option still i get the error as=

/bin/sh ../../libtool --tag=CC   --mode=compile mpCC -DHAVE_CONFIG_H -I.
-I../../src  -I../../include
-DGMXLIBDIR=\"/home/staff/sec/secdpal/soft/gromacs/share/top\"
-I/home/staff/sec/secdpal/soft/include  -O3 -qarch=ppc64 -qtune=pwr5 -c -o
vmdio.lo vmdio.c
 mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\"/home/staff/sec/secdpal/soft/gromacs/share/top\"
-I/home/staff/sec/secdpal/soft/include -O3 -qarch=ppc64 -qtune=pwr5 -c
vmdio.c -o vmdio.o
1506-503 (W) Option "-qlongdouble / -qldbl128" is not supported for LINUX
for Power.
"/usr/include/glob.h", line 166.34: 1506-276 (S) Syntax error: possible
missing identifier?
"/usr/include/glob.h", line 166.12: 1506-033 (S) Function __REDIRECT_NTH is
not valid. Function cannot return a function.
"/usr/include/glob.h", line 166.12: 1506-282 (S) The type of the parameters
must be specified in a prototype.
"/usr/include/glob.h", line 169.35: 1506-334 (S) Identifier glob_t has
already been defined on line 113 of "/usr/include/glob.h".
"/usr/include/glob.h", line 169.42: 1506-277 (S) Syntax error: possible
missing ';' or ','?
"/usr/include/glob.h", line 171.39: 1506-276 (S) Syntax error: possible
missing identifier?
"/usr/include/glob.h", line 171.13: 1506-282 (S) The type of the parameters
must be specified in a prototype.
"/usr/include/glob.h", line 171.13: 1506-343 (S) Redeclaration of
__REDIRECT_NTH differs from previous declaration on line 166 of
"/usr/include/glob.h".
"/usr/include/glob.h", line 171.13: 1506-050 (I) Return type "void" in
redeclaration is not compatible with the previous return type "int(const
char*,int)".
"/usr/include/glob.h", line 171.58: 1506-160 (S) Object globfree64 cannot
be declared as type void.
"/usr/include/glob.h", line 175.12: 1506-343 (S) Redeclaration of glob64
differs from previous declaration on line 169 of "/usr/include/glob.h".
"/usr/include/glob.h", line 175.12: 1506-382 (I) The type "int(const char*
restrict,int,int(*)(const char*,int),struct {...}* restrict)" of identifier
glob64 differs from previous type "int".
make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib && make ; exit 0)
make[1]: Entering directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib'
make[1]: Warning: File `Makefile' has modification time 8.8e+02 s in the
future
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `
libmd_mpi.la'.  Stop.
make[1]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel && make mdrun ; exit 0)
make[1]: Entering directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel'
make[1]: Warning: File `Makefile' has modification time 8.8e+02 s in the
future
/bin/sh ../../libtool --tag=CC   --mode=link mpCC  -O3 -qarch=ppc64
-qtune=pwr5 -no-undefined -version-info 6:0:0
-L/home/staff/sec/secdpal/soft/lib  -o libgmxpreprocess_mpi.la -rpath
/home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo
convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo
gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo
readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo
topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo
vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1
make[1]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel'
make: warning:  Clock skew detected.  Your build may be incomplete.


On Sat, Dec 10, 2011 at 1:05 PM, Mark Abraham wrote:

>  On 10/12/2011 6:31 PM, aiswarya pawar wrote:
>
>
> Hi,
>
> I tried giving this-
>
>
> ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
> --enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3 -qarch=450d
> -qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d -qtune=450"
>
> and the configure process ran well.
>
> but when i gave make mdrun, i get an error which says=
>
> make[2]: *** [vmdio.lo] Error 1
>
>
> The first error happened above this line, so we can't tell what is wrong.
> As a wild guess, use --without-dlopen with configure.
>
> Mark
>
>
> make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/
> gmxlib'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
> (cd ./src/mdlib && make ; exit 0)
> make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib'
> make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the
> future
> make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `
> libmd_mpi.la'.  Stop.
> make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib'
> (cd ./src/k

[gmx-users] qm/mm(orca/gromacs)

[li yan]

Dear Gromacs developers:

I'm trying to run a QM-MM single point energy calculation on a
structure (a small molecule with 50 water molecules with no pbc, no
cutoff). I use orca for QM part amd gromacs for MM part. But when I
run mdrun -nt 1 -s sp.tpr -c sp.gro -g sp.log, the ORCA run quickly
and terminate naormally, but after that mdrun run stops with a
segmentation fault. Here is the error information:

Back Off! I just backed up sp.log to ./#sp.log.1#

Reading file sp.tpr, VERSION 4.5.5 (single precision)

QM/MM calculation requested.

there we go!

Layer 0

nr of QM atoms 9

QMlevel: MP2/3-21G

/home/user/orca_x86_64_exe_r2360/home/user/programs/orca_x86_64_exe_r2360...

orca initialised...

Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up ener.edr to ./#ener.edr.1#

starting mdrun 'Protein'

0 steps,  0.0 ps.

Calling '/home/li/programs/orca_x86_64_exe_r2360/orca
/home/li/Test/test_gmx/qmmm/test/sp.inp >>
/home/li/Test/test_gmx/qmmm/test/sp.out'

Segmentation fault

Here is my sp.mdp

title= test

cpp  =/lib/cpp

integrator   = md

nsteps   = 0

dt   = 0.001

;constraints = none

emtol= 10.0

emstep   = 0.01

nstcomm  = 1

ns-type  = simple

nstlist  = 0

rlist= 0

rcoulomb = 0

rvdw = 0

tcoupl   = no

pcoupl   = no

gen-vel  = no

nstxout  = 1

nstlog   = 1

nstenergy= 1

nstvout  = 1

nstfout  = 1

pbc  = no

comm_mode= angular

; non-equilibrium md

freezegrps   = System

freezedim= y y y

xtc_grps = System

energygrps   = System

;qmmm calculation

QMMM = yes

QMMM-grps= QMatoms

QMMMscheme   = normal

QMmethod = MP2

QMbasis  = 3-21g

QMcharge = 0

QMmult   = 1

The *.ORCAINFO is:

 ! RKS b3lyp/g sv(p) tightscf

And I also tried QMMMsheme=ONIOM, but I get the segmentation fault
too. Am I missing something in all of this?
 or the orca/gromcas can not be used  to non periodic system?
 Any help would be highly appreciated.

Thanks

Yan
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Re: [gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

[David van der Spoel]

On 12/10/11 3:23 AM, Matthew Zwier wrote:

Hi Ruhollah,

A while ago on the list there was a discussion of extreme memory use
and possibly-incorrect results from g_msd under some conditions.  The
problem could be worked around by imaging the trajectory with trjconv
first to remove jumps across the box, then running g_msd on the
results.  Perhaps you'll have some more success with that workflow.


All of this is not necessary.

You should first try to do more tests before you claim a bug. For 
instance, compute the msd of a single Ca atom.


Furthermore you do not state how your simulation was done and how long 
it was. Since you have a single molecule statistics will be poor unless 
you simulate for 100 ns or so.

Cheers,
Matt Z.

On Fri, Dec 9, 2011 at 6:30 PM, Ruhollah Moussavi-Baygi
  wrote:

David,
thank you for your reply.

but, g_msd gives a diffusion coefficient which is one order of magnitude
higher than expected for a small polypeptide (15 res long with gyration Rg ~
0.8nm) with the same size. this is command line i used:
g_msd-mpi -f  md_mine_2nd.xtc -s  md_mine_2nd.tpr -o  msd_2nd.xvg

when visualizing, I can see that the polypeptide crosses the boundary
several times. apparently,  g_msd counts these 'artificial' jumps in MSD
calculation.  and, that's probably why the diffusion coefficient is
calculated such high (i.e. 500 um2/s for a small protein).

if this is the case, it is a bug in g_msd I believe.

is there any way to get round this problem?

-- Forwarded message --
From: Anonymous
Date: Fri, Dec 9, 2011 at 12:17 AM
Subject: Comment for Forum topic: diffusion coefficient
To: ruhollah...@gmail.com


Hi ruhollahmoussavi-baygi,

Comment by davidvanderspoel: diffusion coefficient


On 2011-12-09 08:34, Mark Abraham wrote:

On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote:

I want to calculate the diffusion coefficient of a small polypeptide
with g_msd (see here
http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant [1])

because of periodic boundary condition, when the peptide goes out of
the right side it comes in from left side, which leads to an
artificial displacement. this will give rise to a non-realistic MSD.

is g_msd intelligent enough to avoid this artificial displacement?




Yes it is.



Not sure about g_msd, but you can take care of it yourself with a
workflow derived from the information here

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condi...
[2]


Mark


Read more
http://support.scalalife.eu/content/diffusion-coefficient#comment-103


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[1] http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant
[2]
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions




--
Best,
Ruhollah Moussavi-Baygi

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--
David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se

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[gmx-users] No such moleculetype Na

[Setare Jiji]

Hi,

I am running Tutorial 1: Lysozyme in Water.
I used 4-0-7 version and the sequence is true but in minimization energy step,I 
have this fatal error:
  No such moleculetype Na
so,what do I do?

Best regards

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Re: [gmx-users] No such moleculetype Na

[Tsjerk Wassenaar]

Hi Setare,

That tutorial is made for later gromacs versions, as stated at the
beginning. The naming of ions has changed since 4.0.*.

Cheers,

Tsjerk

On Dec 10, 2011 1:00 PM, "Setare Jiji"  wrote:

Hi,

I am running Tutorial 1: Lysozyme in
Water
.
I used 4-0-7 version and the sequence is true but in minimization energy
step,I have this fatal error:
  No such moleculetype Na
so,what do I do?

Best regards


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[gmx-users] Re: gmx-users Digest, Vol 92, Issue 56

[Gerrit Groenhof]

Does this also happen if you use pbc?
gerrit
On 10 Dec 2011, at 10:59, gmx-users-requ...@gromacs.org wrote:

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> Today's Topics:
> 
>   1. qm/mm(orca/gromacs) (li yan)
> 
> 
> --
> 
> Message: 1
> Date: Sat, 10 Dec 2011 17:59:11 +0800
> From: li yan 
> Subject: [gmx-users] qm/mm(orca/gromacs)
> To: gmx-users@gromacs.org
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear Gromacs developers:
> 
> I'm trying to run a QM-MM single point energy calculation on a
> structure (a small molecule with 50 water molecules with no pbc, no
> cutoff). I use orca for QM part amd gromacs for MM part. But when I
> run mdrun -nt 1 -s sp.tpr -c sp.gro -g sp.log, the ORCA run quickly
> and terminate naormally, but after that mdrun run stops with a
> segmentation fault. Here is the error information:
> 
> Back Off! I just backed up sp.log to ./#sp.log.1#
> 
> Reading file sp.tpr, VERSION 4.5.5 (single precision)
> 
> QM/MM calculation requested.
> 
> there we go!
> 
> Layer 0
> 
> nr of QM atoms 9
> 
> QMlevel: MP2/3-21G
> 
> /home/user/orca_x86_64_exe_r2360/home/user/programs/orca_x86_64_exe_r2360...
> 
> orca initialised...
> 
> Back Off! I just backed up traj.trr to ./#traj.trr.1#
> 
> Back Off! I just backed up ener.edr to ./#ener.edr.1#
> 
> starting mdrun 'Protein'
> 
> 0 steps,  0.0 ps.
> 
> Calling '/home/li/programs/orca_x86_64_exe_r2360/orca
> /home/li/Test/test_gmx/qmmm/test/sp.inp >>
> /home/li/Test/test_gmx/qmmm/test/sp.out'
> 
> Segmentation fault
> 
> Here is my sp.mdp
> 
> title= test
> 
> cpp  =/lib/cpp
> 
> integrator   = md
> 
> nsteps   = 0
> 
> dt   = 0.001
> 
> ;constraints = none
> 
> emtol= 10.0
> 
> emstep   = 0.01
> 
> nstcomm  = 1
> 
> ns-type  = simple
> 
> nstlist  = 0
> 
> rlist= 0
> 
> rcoulomb = 0
> 
> rvdw = 0
> 
> tcoupl   = no
> 
> pcoupl   = no
> 
> gen-vel  = no
> 
> nstxout  = 1
> 
> nstlog   = 1
> 
> nstenergy= 1
> 
> nstvout  = 1
> 
> nstfout  = 1
> 
> pbc  = no
> 
> comm_mode= angular
> 
> ; non-equilibrium md
> 
> freezegrps   = System
> 
> freezedim= y y y
> 
> xtc_grps = System
> 
> energygrps   = System
> 
> ;qmmm calculation
> 
> QMMM = yes
> 
> QMMM-grps= QMatoms
> 
> QMMMscheme   = normal
> 
> QMmethod = MP2
> 
> QMbasis  = 3-21g
> 
> QMcharge = 0
> 
> QMmult   = 1
> 
> The *.ORCAINFO is:
> 
> ! RKS b3lyp/g sv(p) tightscf
> 
> And I also tried QMMMsheme=ONIOM, but I get the segmentation fault
> too. Am I missing something in all of this?
> or the orca/gromcas can not be used  to non periodic system?
> Any help would be highly appreciated.
> 
> Thanks
> 
> Yan
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Re: [gmx-users] No such moleculetype Na

[cuong nguyen]

Hi Setare,

You should find the ions.itp file in your computer, open and see the exact
name of sodium in this file. Use this name when using the command "genion".

Good luck!

Cuong

2011/12/10 Setare Jiji 

>   Hi,
>
> I am running Tutorial 1: Lysozyme in 
> Water
> .
> I used 4-0-7 version and the sequence is true but in minimization energy
> step,I have this fatal error:
>   No such moleculetype Na
> so,what do I do?
>
> Best regards
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
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Mobile: (+61) 452213981
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Re: Re: [gmx-users] Problem with GDP parameters generation

[neeru sharma]

Thanks Mark for the response.

I have contacted the amber mailing list too and I have got the parameters
for GDP in AMBER94 forcefield. But I would need the parameters in AMBER03
forcefield, so that I can use them while running simulations in gromacs.
So, can I use the same parameters of AMBER94 in AMBER03 too?

Neeru

>
> On 10/12/2011 6:25 AM, neeru sharma wrote:
> > Dear gromacs users,
> >
> > I have to simulate a protein-GDP complex using gromacs.As PRODRG was
> > giving unreliable output, I generated Amber topology and coordinate
> > files for GTP molecule. Then, I converted them into the corresponding
> > gromacs topology (.top) and coordinate files (.gro) and generated
> > parameter (.itp) file using following command (Thanks to Tsjerk):
> > sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e
> > '/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP
> >
> > But the topology and co-ordinates file are quite different from the
> > input PDB file and hence the parameters are also faulty, the GDP
> > molecule is not fitting in the binding pocket of protein. Upon
> > tracking the whole process, it was found that the error might be while
> > using antechamber for generating prepin file using Gaussian output
> > file as the input.
> >
> > Can anyone please suggest some way to apply some constraints in the
> > antechamber command itself. OR if anybody has the paramters or
> > topology for GDP, can anyone provide me the same so that I can compare
> > and see where the parameters are differing.
>
> Surely antechamber will accept whatever coordinate file you provide to
> it, and the AMBER mailing list is the place to make inquiries about it
> (after checking the documentation).
>
> Don't stress too much about the charges - those that are suitable in the
> bound and unbound form will normally be different, and current methods
> can't access the former.
>
> Mark
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Re: [gmx-users] Problem with GDP parameters generation

[Mark Abraham]

On 11/12/2011 1:09 AM, neeru sharma wrote:

Thanks Mark for the response.

I have contacted the amber mailing list too and I have got the 
parameters for GDP in AMBER94 forcefield. But I would need the 
parameters in AMBER03 forcefield, so that I can use them while running 
simulations in gromacs. So, can I use the same parameters of AMBER94 
in AMBER03 too?


Probably not, but you should go and read the papers in which the 
development of each was described and make your own judgement. The 
availability of parameters can be a sound reason for the choice of force 
field.


Mark



Neeru


On 10/12/2011 6:25 AM, neeru sharma wrote:
> Dear gromacs users,
>
> I have to simulate a protein-GDP complex using gromacs.As PRODRG was
> giving unreliable output, I generated Amber topology and coordinate
> files for GTP molecule. Then, I converted them into the
corresponding
> gromacs topology (.top) and coordinate files (.gro) and generated
> parameter (.itp) file using following command (Thanks to Tsjerk):
> sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e
> '/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP
>
> But the topology and co-ordinates file are quite different from the
> input PDB file and hence the parameters are also faulty, the GDP
> molecule is not fitting in the binding pocket of protein. Upon
> tracking the whole process, it was found that the error might be
while
> using antechamber for generating prepin file using Gaussian output
> file as the input.
>
> Can anyone please suggest some way to apply some constraints in the
> antechamber command itself. OR if anybody has the paramters or
> topology for GDP, can anyone provide me the same so that I can
compare
> and see where the parameters are differing.

Surely antechamber will accept whatever coordinate file you provide to
it, and the AMBER mailing list is the place to make inquiries about it
(after checking the documentation).

Don't stress too much about the charges - those that are suitable
in the
bound and unbound form will normally be different, and current methods
can't access the former.

Mark
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Re: [gmx-users] mdrun_mpi error

[Mark Abraham]

On 10/12/2011 7:54 PM, aiswarya pawar wrote:

i used the option still i get the error as=

/bin/sh ../../libtool --tag=CC   --mode=compile mpCC -DHAVE_CONFIG_H 
-I. -I../../src  -I../../include 
-DGMXLIBDIR=\"/home/staff/sec/secdpal/soft/gromacs/share/top\" 
-I/home/staff/sec/secdpal/soft/include  -O3 -qarch=ppc64 -qtune=pwr5 
-c -o vmdio.lo vmdio.c


This is a build failure optimizing for POWER5. The configure line you 
gave below was optimizing for BlueGene/P. We can't help if we don't know 
what your context is. Start a new email and describe one single problem 
fully in it.


Mark

 mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include 
-DGMXLIBDIR=\"/home/staff/sec/secdpal/soft/gromacs/share/top\" 
-I/home/staff/sec/secdpal/soft/include -O3 -qarch=ppc64 -qtune=pwr5 -c 
vmdio.c -o vmdio.o
1506-503 (W) Option "-qlongdouble / -qldbl128" is not supported for 
LINUX for Power.
"/usr/include/glob.h", line 166.34: 1506-276 (S) Syntax error: 
possible missing identifier?
"/usr/include/glob.h", line 166.12: 1506-033 (S) Function 
__REDIRECT_NTH is not valid. Function cannot return a function.
"/usr/include/glob.h", line 166.12: 1506-282 (S) The type of the 
parameters must be specified in a prototype.
"/usr/include/glob.h", line 169.35: 1506-334 (S) Identifier glob_t has 
already been defined on line 113 of "/usr/include/glob.h".
"/usr/include/glob.h", line 169.42: 1506-277 (S) Syntax error: 
possible missing ';' or ','?
"/usr/include/glob.h", line 171.39: 1506-276 (S) Syntax error: 
possible missing identifier?
"/usr/include/glob.h", line 171.13: 1506-282 (S) The type of the 
parameters must be specified in a prototype.
"/usr/include/glob.h", line 171.13: 1506-343 (S) Redeclaration of 
__REDIRECT_NTH differs from previous declaration on line 166 of 
"/usr/include/glob.h".
"/usr/include/glob.h", line 171.13: 1506-050 (I) Return type "void" in 
redeclaration is not compatible with the previous return type 
"int(const char*,int)".
"/usr/include/glob.h", line 171.58: 1506-160 (S) Object globfree64 
cannot be declared as type void.
"/usr/include/glob.h", line 175.12: 1506-343 (S) Redeclaration of 
glob64 differs from previous declaration on line 169 of 
"/usr/include/glob.h".
"/usr/include/glob.h", line 175.12: 1506-382 (I) The type "int(const 
char* restrict,int,int(*)(const char*,int),struct {...}* restrict)" of 
identifier glob64 differs from previous type "int".

make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory 
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib'

make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory 
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib'

(cd ./src/mdlib && make ; exit 0)
make[1]: Entering directory 
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib'
make[1]: Warning: File `Makefile' has modification time 8.8e+02 s in 
the future
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la 
', needed by `libmd_mpi.la 
'.  Stop.
make[1]: Leaving directory 
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib'

(cd ./src/kernel && make mdrun ; exit 0)
make[1]: Entering directory 
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel'
make[1]: Warning: File `Makefile' has modification time 8.8e+02 s in 
the future
/bin/sh ../../libtool --tag=CC   --mode=link mpCC  -O3 -qarch=ppc64 
-qtune=pwr5 -no-undefined -version-info 6:0:0  
-L/home/staff/sec/secdpal/soft/lib  -o libgmxpreprocess_mpi.la 
 -rpath 
/home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo 
convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo 
gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo 
pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo 
specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo 
toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo 
../mdlib/libmd_mpi.la  -lnsl -lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la 
' or unhandled argument `../mdlib/libmd_mpi.la 
'
make[1]: *** [libgmxpreprocess_mpi.la 
] Error 1
make[1]: Leaving directory 
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel'

make: warning:  Clock skew detected.  Your build may be incomplete.


On Sat, Dec 10, 2011 at 1:05 PM, Mark Abraham > wrote:


On 10/12/2011 6:31 PM, aiswarya pawar wrote:


Hi,

I tried giving this-


./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
--enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3
-qarch=450d -qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d
-qtune=450"

and the configure process ran well.

but when i gave make mdrun, i get an error which says=

make[2]: *** [vmdio.lo] Error 1


The first error happened above this line, so we can't tell what is
wrong. As a wild guess, use --without-dlopen with