date:20130616

[gmx-users] Gromacs 4.5.5

2013-06-16 Thread Emmanuel, Alaina

Dear All, 

I've had to re-install my gromacs on my computer and I'm having issues getting 
past the "Making all in Man7" during the "make" stage. Below (at the end) are 2 
copies of different outputs I get during my installation. The first copy is 
from the "make.log" file. The second copy is from typing "grep -i error 
make.log". 

The stages that I have followed so far are: 

1) tar -xvf gromacs-4.5.5.tar.gz
2) cd gromacs-4.5.5
3) ./configure --prefix=/home/user/name/gromacs --disable-float
4) make > make.log &
5) grep -i error make.log

If I delete the "man7" folder in the second stage, I have no problem completing 
the installation of gromacs. Unfourtunately this means that I am only able to 
use about half of the g_analysis_tools available.  In addition to this I'm only 
able to use them whilst in the same directory. 


Output from "make > make.log"

make[3]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share/template'
make[2]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share/template'
Making all in html
make[2]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/share/html'
Making all in .
make[3]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/share/html'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share/html'
Making all in images
make[3]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/share/html/images'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share/html/images'
Making all in online
make[3]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/share/html/online'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share/html/online'
make[2]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share/html'
make[2]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/share'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share'
make[1]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/share'
Making all in man
make[1]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/man'
Making all in man1
make[2]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/man/man1'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/man/man1'
Making all in man7
make[2]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/man/man7'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/man/man7'
make[2]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5/man'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/man'
make[1]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5/man'
make[1]: Entering directory `/home/chem/msrhcf/gromacs-4.5.5'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/home/chem/msrhcf/gromacs-4.5.5'


Lengthy output for "grep -i error make.log":

/bin/sh ../../libtool --tag=CC   --mode=compile cc  -DHAVE_CONFIG_H -I. 
-I../../src -I/usr/include/libxml2 -I../../include 
-DGMXLIBDIR=\"/home/chem/msrhcf/gromacs_from455/share/top\"   -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 
-funroll-all-loops -std=gnu99 -pthread -I./include -MT gmx_pme_error.lo -MD -MP 
-MF .deps/gmx_pme_error.Tpo -c -o gmx_pme_error.lo gmx_pme_error.c  

 cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include 
-DGMXLIBDIR=\"/home/chem/msrhcf/gromacs_from455/share/top\" -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 
-funroll-all-loops -std=gnu99 -pthread -I./include -MT gmx_pme_error.lo -MD -MP 
-MF .deps/gmx_pme_error.Tpo -c gmx_pme_error.c  -fPIC -DPIC -o 
.libs/gmx_pme_error.o   
   
 cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include 
-DGMXLIBDIR=\"/home/chem/msrhcf/gromacs_from455/share/top\" -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 
-funroll-all-loops -std=gnu99 -pthread -I./include -MT gmx_pme_error.lo -MD -MP 
-MF .deps/gmx_pme_error.Tpo -c gmx_pme_error.c -o gmx_pme_error.o >/dev/null 
2>&1
 
mv -f .deps/gmx_pme_error.Tpo .deps/gmx_pme_error.Plo   
  
/bin/sh ../../libtool --tag=CC   --mode=link cc   -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 
-pthread -I./include -no-undefined -version-info 6:0:0   -o libgmxana_d.la 
-rpath /home/chem/msrhcf/gromacs_from455/lib geminate.lo autocorr.lo expfit.lo 
polynomials.lo levenmar.lo anadih.lo pp2shift.lo dlist.lo eigio.lo cmat.lo 
eigensolver.lo nsc.lo hxprops.lo fitahx.lo gmx_analyze.lo gmx_anaeig.lo 
gmx_bar.lo gmx_angle.lo gmx_bond.lo gmx_bundle.lo gmx_chi.lo gmx_cluster.lo

[gmx-users] Distance.dat file in umbrella sampling

2013-06-16 Thread Kieu Thu Nguyen

Dear Justin,

I am testing a umbrella simulation basing on your tutorial. But after using
your distances.pl script, i do not have the file "summary_distances.dat".
It only makes many xvg files.
I post the script below:

#!/usr/bin/perl -w

use strict;

# loop g_dist command - measure distance in each frame, write to a file
for (my $i=0; $i<=500; $i++) {
print "Processing configuration $i...\n";
system("g_dist_mpi_d -s pull.tpr -f conf${i}.gro -n index.ndx -o
dist${i}.xvg < groups.txt &>/dev/null");
}

# write output to single file
open(OUT, ">>summary_distances.dat");

for (my $j=0; $j<=500; $j++) {
open(IN, ";

my $distance;

foreach $_ (@array) {
if ($_ =~ /[#@]/) {
# do nothing, it's a comment or formatting line
} else {
my @line = split(" ", $_);
$distance = $line[1];
}
}

close(IN);
print OUT "$j\t$distance\n";
}

close(OUT);

# clean up
print "Cleaning up...\n";

for (my $k=0; $k<=500; $k++) {
unlink "dist${k}.xvg";
}

exit;


Do i have to modify the script ?


Thankful and regards,

Thu
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Re: [gmx-users] Distance.dat file in umbrella sampling

2013-06-16 Thread Justin Lemkul




On 6/16/13 7:47 PM, Kieu Thu Nguyen wrote:

Dear Justin,

I am testing a umbrella simulation basing on your tutorial. But after using
your distances.pl script, i do not have the file "summary_distances.dat".
It only makes many xvg files.
I post the script below:

#!/usr/bin/perl -w

use strict;

# loop g_dist command - measure distance in each frame, write to a file
for (my $i=0; $i<=500; $i++) {
 print "Processing configuration $i...\n";
 system("g_dist_mpi_d -s pull.tpr -f conf${i}.gro -n index.ndx -o
dist${i}.xvg < groups.txt &>/dev/null");
}

# write output to single file
open(OUT, ">>summary_distances.dat");

for (my $j=0; $j<=500; $j++) {
 open(IN, ";

 my $distance;

 foreach $_ (@array) {
 if ($_ =~ /[#@]/) {
 # do nothing, it's a comment or formatting line
 } else {
 my @line = split(" ", $_);
 $distance = $line[1];
 }
 }

 close(IN);
 print OUT "$j\t$distance\n";
}

close(OUT);

# clean up
print "Cleaning up...\n";

for (my $k=0; $k<=500; $k++) {
 unlink "dist${k}.xvg";
}

exit;


Do i have to modify the script ?



You already have.  My script doesn't use a double-precision/MPI version of 
g_dist.  MPI has no effect for anything except mdrun, FYI.  In principle, this 
isn't a big deal, unless the MPI compilation has rendered g_dist damaged in some 
way.


Run one invocation of g_dist manually.  There's got to be some error occurring 
somewhere, but the script won't tell you that.  If you have .xvg files when the 
script is done, that's also wrong, since all of them should be deleted by the 
last for-loop.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Re: Gromacs 4.5.5

2013-06-16 Thread maggin

Hi, Alaina 

Before you install GMX4.5.5, did you install cmake-2.8.8 and fftw-3.3.2 ?

maggin



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[gmx-users] NVT .gro for NPT

2013-06-16 Thread maggin

Hi, all

I run a small peptide, and after NVT, I got the XXX.gro file like this,

 

because the peptide not at the center of box, I use this .gro to run NPT, if
it reasonable?

If it's not good, how can I avoid such phenomenon?

Thank you very much!

maggin



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[gmx-users] a snapshot of NVT

2013-06-16 Thread maggin

Hi, all

When I run a small peptide at NVT stage, I get a snapshot like this:

 

I am not sure if it right, and can I use it for NPT ?

Thank you very much!

maggin



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Re: [gmx-users] NVT .gro for NPT

2013-06-16 Thread Tsjerk Wassenaar

Hi Maggin,

Why would that be a problem?

Tsjerk



On Mon, Jun 17, 2013 at 7:28 AM, maggin  wrote:

> Hi, all
>
> I run a small peptide, and after NVT, I got the XXX.gro file like this,
>
> 
>
> because the peptide not at the center of box, I use this .gro to run NPT,
> if
> it reasonable?
>
> If it's not good, how can I avoid such phenomenon?
>
> Thank you very much!
>
> maggin
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/NVT-gro-for-NPT-tp5009205.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] a snapshot of NVT

2013-06-16 Thread Tsjerk Wassenaar

Hi Maggin,

Okay, this image may require a bit of explanation :p VMD has drawn bonds
according to the bondedness in a reference file. But the atoms have moved,
and some went over the box boundaries. So they show up with long bonds
crossing the whole box. It's not a problem, just a visualization artefact.

Cheers,

Tsjerk


On Mon, Jun 17, 2013 at 7:52 AM, maggin  wrote:

> Hi, all
>
> When I run a small peptide at NVT stage, I get a snapshot like this:
>
> 
>
> I am not sure if it right, and can I use it for NPT ?
>
> Thank you very much!
>
> maggin
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/a-snapshot-of-NVT-tp5009206.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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>



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[gmx-users] a snapshot of NVT

2013-06-16 Thread maggin

Hi, all

When I run a small peptide at NVT stage, I get a snapshot like this:

 

I am not sure if it right, and can I use it for NPT ?

Thank you very much!

maggin



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[gmx-users] Re: NVT .gro for NPT

2013-06-16 Thread maggin

Hi, Tsjerk 

You asked me a good question. 

Ya, sometime it accords my imagination to tell if it right or not. That's
not the correct way.

Maybe it  near boundary, like at the boundary of dangerous. So let me have
such question. 

maggin



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[gmx-users] Re: a snapshot of NVT

2013-06-16 Thread maggin

Hi,Tsjerk,

Oh, that's it !

Thank you very much for your kind help!

maggin



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Re: [gmx-users] Re: Gromacs 4.5.5

2013-06-16 Thread Mark Abraham

On Jun 17, 2013 5:50 AM, "maggin"  wrote:
>
> Hi, Alaina
>
> Before you install GMX4.5.5, did you install cmake-2.8.8 and fftw-3.3.2 ?

Installing cmake for an autotools build isn't going to help ;-)

Mark

>
> maggin
>
>
>
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[gmx-users] Gromacs 4.5.5

[gmx-users] Distance.dat file in umbrella sampling

Re: [gmx-users] Distance.dat file in umbrella sampling

[gmx-users] Re: Gromacs 4.5.5

[gmx-users] NVT .gro for NPT

[gmx-users] a snapshot of NVT

Re: [gmx-users] NVT .gro for NPT

Re: [gmx-users] a snapshot of NVT

[gmx-users] a snapshot of NVT

[gmx-users] Re: NVT .gro for NPT

[gmx-users] Re: a snapshot of NVT

Re: [gmx-users] Re: Gromacs 4.5.5

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