Re: [gmx-users] residue SASA

[Diego Enry Gomes]

This is what I mean by "quick and dirty".

#!/bin/bash
# Reads the output of "g_sas" per residue (-or) and writes only the residues 
you want.   
# Diego E.B. Gomes, Roberto D. Lins, Pedro G. Pascutti, Thereza A. Soares
# mailto: di...@biof.ufrj.br 

#1 ) To perform multiple g_sas  (will write out all residues in many files)
for ((frame=0;frame<=10;frame=frame+1)) do
g_sas_4 -s md.tpr -f md.xtc -n index.ndx -or resarea.${frame} -o area.${frame} 
-oa atomarea.${frame} -b ${frame} -e ${frame} < resarea.favorites.dat

  for ((frame=0;frame<=1000;frame=frame+1)) do
echo -ne "$frame \r"
cat resarea.${frame}.xvg |grep -v "#" |grep -v "@" > tmp

i=1
while read a b c ; do # reads the text file
  residue[$i]=$a
  sas[$i]=$b
  stdev[$i]=$c
  i=$(($i+1))
done < "tmp"

j=1
for i in `echo $list` ; do
  out[$j]=${sas[$i]}
  j=$(($i+1))
done

echo $frame ${out[@]} >> resarea.favorites.dat

  done
done

# :) 

On Jul 7, 2011, at 9:17 PM, Justin A. Lemkul wrote:

> 
> 
> ahmet yıldırım wrote:
>> There are hydrophilic and hydrophobic SASA values versus simulation time in 
>> the output file (area.xvg). I want to hydrophilic and hydrophobic SASA 
>> values versus residue.
> 
> That's not implemented, but it would probably be rather easy to modify the 
> code to do so.
> 
> -Justin
> 
>> 2011/7/7 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>ahmet yıldırım wrote:
>>Dear users,
>>I want to calculate hydrophilic and hyrophobic SASA value of
>>each residue in protein. I used a command as the following:
>>g_sas -f run.xtc -s run.tpr -or protein_protein.xvg
>>Select a group for calculation of surface and a group for output
>>select a group: 1 (protein)
>>select a group: 2 (protein)
>>But there is SASA value of each residue in the output file. How
>>can I seperate the residues as a hydrophilic and hyrophobic SASA?
>>This is already in the output file.  Check the legends of area.xvg
>>and you will see.
>>-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/__Support/Mailing_Lists/Search
>> before posting!
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>>interface or send it to gmx-users-requ...@gromacs.org
>>.
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>>
>> -- 
>> Ahmet YILDIRIM
> 
> -- 
> 
> 
> 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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--
Diego E. B. Gomes
Instituto de Biofísica Carlos Chagas Filho
Universidade Federal do Rio de Janeiro
Brasil   +55 21 2562.6507

/temp @ Laboratoire de Biologie et de Pharmacologie Appliquée 
Ecole Normale Supérieure, Cachan, France
France +33 07 8638.8099




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Re: [gmx-users] residue SASA

[Diego Enry Gomes]

There's a quick & dirty workaround. You can write a script to "g_sas" each 
frame individually, writing many output files. Then grab the results from there.


Sent from my iPhone

On Jul 7, 2011, at 9:17 PM, "Justin A. Lemkul"  wrote:

> 
> 
> ahmet yıldırım wrote:
>> There are hydrophilic and hydrophobic SASA values versus simulation time in 
>> the output file (area.xvg). I want to hydrophilic and hydrophobic SASA 
>> values versus residue.
> 
> That's not implemented, but it would probably be rather easy to modify the 
> code to do so.
> 
> -Justin
> 
>> 2011/7/7 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>ahmet yıldırım wrote:
>>Dear users,
>>I want to calculate hydrophilic and hyrophobic SASA value of
>>each residue in protein. I used a command as the following:
>>g_sas -f run.xtc -s run.tpr -or protein_protein.xvg
>>Select a group for calculation of surface and a group for output
>>select a group: 1 (protein)
>>select a group: 2 (protein)
>>But there is SASA value of each residue in the output file. How
>>can I seperate the residues as a hydrophilic and hyrophobic SASA?
>>This is already in the output file.  Check the legends of area.xvg
>>and you will see.
>>-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/__Support/Mailing_Lists/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/__Support/Mailing_Lists
>>
>> -- 
>> Ahmet YILDIRIM
> 
> -- 
> 
> 
> 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] installation of gromacs

[Diego Enry]

You got this wrong
export CPPFLAGS="-I/home/local/fftw/include"
export LDFLAGS="-L/home/local/fftw/lib"

replace by this
export CPPFLAGS="-I$HOME/local/fftw/include"
export LDFLAGS="-L$HOME/local/fftw/lib"


On Thu, Mar 17, 2011 at 12:24 PM, Thomas Koller  wrote:
> Now I get this again:
>
> checking for fftw3.h... configure: error: Cannot find the default external 
> FFT library (fftw3).
>
> Please follow my way:
>
> i) I unpacke fftw and gromacs to two folders.
> iii) I go the the fftw folder and make:
>    - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared   
> --enable-float
>    - make -j
>    - make install
>    - export CPPFLAGS="-I/home/local/fftw/include"
>    - export LDFLAGS="-L/home/local/fftw/lib"
>
> iii) Then I go (cd) to the folder gromacs-4.0.7
>    - ./configure --prefix=$HOME/local/gromacs
>    - Now I get the error writen above.
>
> Is my way wrong, do I have to insert the fftw folder into the gromacs folder, 
> is the sequence wrong?
>
> I wish I can have access soon. :(
>
> Thomas
>
> --
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> belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de
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>



-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] installation of gromacs

[Diego Enry]

Hi Thomas, please send the complete config.log. After you try what I
suggest bellow.
I guess the environment variables for compilers and libs are not set
correctly, not your fault, we'll check on the config file.


#make sure your're usnig bash
bash

#export the regular variables
export CPPFLAGS="-I$HOME/local/fftw3/include"
export LDFLAGS="-L$HOME/local/fftw3/lib"

#also try this one
export LD_LIBRARY_PATH="$HOME/local/fftw3/lib"

#and by now, remove the  --enable-shared
./configure --prefix=$HOME/local/gromacs


On Thu, Mar 17, 2011 at 10:44 AM, Thomas Koller  wrote:
> Hi Nuno,
>
> I have still problems with the insatllation of the 4.0.7 version.
>
> After unpacking of fftw and gromacs, I did:
>
> In the fftw folder:
>
> ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared 
> --enable-float
> make -j
> make install
> export CPPFLAGS="-I$HOME/local/fftw3/include"
> export LDFLAGS="-L$HOME/local/fftw3/lib"
>
> In the gromacs-4.0.7 folder:
>
> ./configure --prefix=$HOME/local/gromacs --enable-shared
>
> At the end I get:
>
> checking for void*... yes
> checking size of void*... configure: error: cannot compute sizeof (void*)
>
> What does that mean? Why is this not working?
>
> Regards,
> Thomas
> --
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>



-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] installation of gromacs

[Diego Enry]

The most basic question is: did you install FFTW as root or superuser ?

sudo make install


If so, try to provide fftw /lib and /include locations (using CPPFLAGS
and LDFLAGS) while configuring GMX. (from the Installation
Instructions)

setenv CPPFLAGS -I/home/joe/fftw/include
setenv LDFLAGS -L/home/joe/fftw/lib

If your shell is bash:

export CPPFLAGS="-I/home/joe/fftw/include"
export LDFLAGS="-L/home/joe/fftw/lib"


*If that does not work. Follow cmake instructions.
http://www.gromacs.org/Developer_Zone/Cmake


** I have this problem with ubuntu 10.04, even though FFTW is ok I can
only Cmake finds fftw. (even providing CPPFLAGS and LDFLAGS)



On Mon, Mar 14, 2011 at 1:05 PM, Thomas Koller  wrote:
> Hello,
>
> I want to install Gromacs 4.5.3 in my computer. Therefore I downloaded fftw 
> 3.2.2 and did as in the instructions:
>
> ./configure --enable-float
> make
> make install
>
> After that I ran:
>
> ./configure
>
> with Gromacs, but I always get:
>
> checking for fftw3.h... configure: error: Cannot find the default external 
> FFT library (fftw3).
> Other alternatives are 'fftw2', or 'mkl' for Intel MKL.
> You are STRONGLY recommended to use one of these - fftw is free.
>
> make is not working after this:
>
> make: *** No targets specified and no makefile found.  Stop.
>
> What is going wrong?
>
> Thomas
> --
> Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] Re: server_for_Gaussian

[Diego Enry]

You can benefit from the WebMO server. It will not run very
"expensive" jobs but is a handy !

http://www.webmo.net/

Support for Gamess 1999+, Gaussian 94/98/03/09, MolPro 2002/2006/2009,
Mopac 7/93/200X, NWChem 4/5, PQS 3.3, PSI 3+, QChem 2/3, and Tinker
4/5

On Thu, Feb 10, 2011 at 12:43 PM, Thomas Schlesier  wrote:
>
>>
>> Message: 2
>> Date: Thu, 10 Feb 2011 16:10:45 +0530
>> From: shahid nayeem
>> Subject: [gmx-users] server_for_Gaussian
>> To: Discussion list for GROMACS users
>> Message-ID:
>>        
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Dear All
>>
>> If any one is aware of a server on which one can upload job for
>> running Gaussian, Please let me know. This I need to modify charges in
>>  the topology file created by ProDrg server.
>> Shahid Nayeem
>>
>
> here is one:
> http://q4md-forcefieldtools.org/REDS/
> you can also directly calculated there resp charges. But if you use resp
> charges, it would be better to also change the force-field (since
> gromos-ff's are for their empirical charges and not resp-charges).
> you could use for example amber's gaff force-field, which uses resp charges.
> see amber/gaff page for more information.
>
> greetings
> thomas
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.

/home/temp @ Ecole Normale Superieure de Cachan, France
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Re: [gmx-users] XTC file not being created, while TRR file is

[Diego Enry]

Hi João, I don't remember EM runs ever producing .xtc files, maybe to
prevent people to use them when "grompp'ing" in the next step. (they're at
much lower precision)

Anyway, that would be nice in case you want to see what's going on during
EM.


On Fri, Jan 7, 2011 at 7:02 PM, João Rodrigues  wrote:

> Hello all,
>
> I'm trying to run energy minimization on my system (protein complex). Since
> it's a bit big (produces 2GB of trr files using l-bfgs) I'm trying to
> supress most of this output and replace the trr file with an xtc file.
>
> I'm using these options in my mdp file (output related):
>
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstcalcenergy   = 0
> nstlog  = 0
> nstenergy   = 0
> nstxtcout   = 10
> xtc-precision   = 1000
>
> Still, I get no xtc file (even if I explicitly run mdrun with the -x
> option) and I still get a large trr file.
>
> Am I doing something wrong?
>
> Best!
>
> João Rodrigues
>
>
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-- 
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Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] make install-mdrun

[Diego Enry Gomes]

get gromacs 4.04

Confirm if you changed the permissions correctly and can write  
anywhere in /usr/local/


Are you doing this as 'root'  or super user (sudo) ? Because if you  
are just a regular user, will won't be able to change the permissions  
in /usr/local/. So, configure gmx to be installed in your local dir.


./configure --prefix=/global/home/pirzadeh/gmx404


On May 8, 2009, at 10:10 AM, Payman Pirzadeh wrote:


Hi All,
I realized that I am missing (Lib and bin folders) analysis tools  
and mdrun MPI. I re-installed the GROMACS 4.0.3, and I found that  
when I get to ‘make install-mdrun’ the following messages show up  
( I am just copying last lines):


make[2]: *** [install-libLTLIBRARIES] Error 1
make[2]: Leaving directory `/global/home/pirzadeh/GROMACS4.0.3/ 
gromacs/src/mdlib'

make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/global/home/pirzadeh/GROMACS4.0.3/ 
gromacs/src/mdlib'

(cd ./src/kernel && make install-mdrun ; exit 0)
make[1]: Entering directory `/global/home/pirzadeh/GROMACS4.0.3/ 
gromacs/src/kernel'

/bin/sh ../../config/mkinstalldirs /usr/local/gromacs/bin
mkdir -p -- /usr/local/gromacs/bin
mkdir: cannot create directory `/usr/local/gromacs': Permission denied
make[1]: *** [install-mdrun] Error 1
make[1]: Leaving directory `/global/home/pirzadeh/GROMACS4.0.3/ 
gromacs/src/kernel'


I changed the permissions and I am still receiving the same message.  
I will e appreciated if someone tell me what is going wrong?!


Payman
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Re: [gmx-users] do_dssp fatal error

[Diego Enry Gomes]

Did you download the "dssp" software from here ?
http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi


On Mar 10, 2009, at 1:12 AM, Homa Azizian wrote:



Hi

when I use do_dssp the following error come:

Program do_dssp, VERSION 4.0.3
Source code file: do_dssp.c, line: 471

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro

/dev/null 2> /dev/null


How could I fix this.
Thank you in advance.
--
Tehran University of Medical Sciences
www.tums.ac.ir


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Re: [gmx-users] problem in pdb file after SA

[Diego Enry Gomes]

You mean that half the protein is in one side of your cubic box and  
the other half is on the other side ?
Try removing PBC or fitting to a reference frame (like the one before  
SA). Search the list archives, this is a very common question.



On Mar 9, 2009, at 10:17 PM, Homa Azizian wrote:



I have done MD job on a 226 residue protein with cubic box -d 0.9 in  
the

editconf step.
after 30 ns I entered the last step pdb to the simulating annealing,  
again
with cubic box and -d 0.9. the highest temp was 600 K and the loest  
was 50 K.
When I see the pdb of structures at 300 K, 600 K and 50 K in pymol,  
it seems
the structures converts to 2 part, one along oneside of cubic's  
surface the
other was in the parallel side, I mean that the system move out of  
the cubic,
and the outer part appears in another side of cubic, so I dont have  
the

integrate structure.
How can I fix this problem.


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Re: [gmx-users] Isn't dt=0.0001 very small?

[Diego Enry Gomes]

Hi Andrew, I have just repeated this tutorial. There is nothing wrong  
with that.


Download all the files again and repeat the tutorial from the beginning.
It can be a file that was corrupted during your previous download or  
you did something wrong in one of the steps.


You can copy&paste the following lines to your terminal. Sit down and  
relax.

If that doesn't work you have a problem with your gromacs installation.


#start copy

wget http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/1LYD.pdb
wget http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/em.mdp
wget http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/pr.mdp
wget http://lindahl.sbc.su.se/outgoing/workshop2007/tutorial1/run.mdp

#run the whole thing
echo 5 | pdb2gmx -f 1LYD.pdb -water tip3p
editconf -f conf.gro –bt dodecahedron –d 0.5 –o box.gro
genbox_d -cs -cp box.gro -p topol.top -o solvated.gro
grompp -v -f em.mdp -c solvated.gro -p topol.top -o em
mdrun -v -deffnm em
grompp -v -f pr.mdp -c em.gro -t em.trr -p topol.top -o pr
mdrun -v -deffnm pr
grompp -v -f run.mdp -c pr.gro -t pr.trr -p topol.top -o md
mdrun -v -deffnm md

#end copy



Diego.

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/tmp/home/@ Pacific Northwest National Laboratory
Richland, WA.  +1 (509) 372.6363
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=

On Mar 10, 2009, at 12:36 AM, Andrew Voronkov wrote:


Dear GROMACS users,
I'm doing this tutorial:
https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
and I have an error with dt=0.002 or even dt=0.001 in pr.mdp during  
equilibration. It works only with dt=0.0001 which seems very very  
small step for me. Is it ok or I need to clean up the warnings like  
in error below(it's for dt=0.002):


starting mdrun 'T4-*LYPOZYME in water'
25000 steps, 50.0 ps.
Warning: 1-4 interaction between 2 and 20 at distance 2.619 which is  
larger than the 1-4 table size 2.000 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

t = 0.000 ps: Water molecule starting at atom 100062 can not be  
settled.

Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
Wrote pdb files with previous and current coordinates
step 0Segmentation fault
and...@linux-f29d:~/GROMACS_MD/1LYD>

Here is pr.mdp:

integrator = md
nsteps = 25000
dt = 0.001
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
tcoupl = Berendsen
tc-grps = protein non-protein
tau-t = 0.1 0.1
ref-t = 298 298
Pcoupl = Berendsen
tau-p = 1.0
compressibility = 5e-5 5e-5 5e-5 0 0 0
ref-p = 1.0
nstenergy = 100
define = -DPOSRES


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Re: [gmx-users] question about parallel runing of gromacs

[Diego Enry Gomes]

On Mar 9, 2009, at 5:12 PM, Mark Abraham wrote:


Xiang Mao wrote:
My PC has a intel core2 cpu. I compiled gromacs under cygwin, and  
using MPICH2. After mpiboot, I use mpirun -n 2 mdrun_mpi  to  
run EM, MD.


OK that might be working right. Now you need to look in the log file  
for an indication of whether the run has two component processes or  
one - right at the top, usually.


Mark


Hi Xiang, maybe the solution is simple and you just didn't use the "-- 
enable-mpi" flag in the ./configure step.

That explains the duplicate steps.

Try a quick "ldd" test to check if MPI compilation worked.

% which mdrun_mpi (find where mdrun was installed, mine is at /usr/ 
local/gmx4/bin/)

% ldd /usr/local/gmx4/bin/mdrun_mpi

You should see "libmpi.so.0" in the list of libraries, if not, go back  
to the ./configure step.



Diego

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Richland, WA.  +1 (509) 372.6363
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Re: [gmx-users] gromacs in parallel version

[Diego Enry Gomes]

Looks like you are using MPICH2 as "mpi" software.
Try including "mpirun" before mdrun_mpi.

mpirun -n 4 mdun_mpi -v -s topol.tpr


If that doesn't work you shoud run start the MPI DAEMON ( MPD ) before  
mpirun:


mpdboot
mpirun -n 2 mdun_mpi -v -s topol.tpr

after you job finishes you might want to stop the mpi daemon by running:
mpdallexit

Diego.

--
=====
Diego Enry B Gomes | PhD Student @ UFRJ - Brazil
/tmp/home/@ Pacific Northwest National Laboratory
Richland, WA.  +1 (509) 372.6363
diegoenry.go...@pnl.gov
=


On Mar 6, 2009, at 5:13 AM, ANINDITA GAYEN wrote:


Dear all,
Sorry for the former post without any subject.
I want to install gromacs in parallel version. I already  
have the normal version of gromacs and i want an MPI version of  
mdrun. The commands i have used are as followed.

make distclean
./configure --enable-float --enable-mpi --prefix=/home/x --program- 
suffix=_mpi

make mdrun -j 4
make install-mdrun
[ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and  
in .bashrc include ...

   export CPPFLAGS=-I/home/x/fftw-3.2.1/include
   export LDFFLAGS=-L/home/x/fftw-3.2.1/lib]
grmmacs installation run successfully.
But when i run
mdrun_mpi ..i got the message  "Can't read  
MPIRUN_MPD" and the mdrun_mpi program does not run.

Any suggestion regarding this problem will be highly acceptable.
thanks in advance,

Ms. Anindita Gayen
C/O Dr. Chaitali Mukhopadhyay
Senior Research Fellow
Department of Chemistry
University of Calcutta
92, A. P. C. Road
Kolkata-700 009
India

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Re: [gmx-users] running GROMACS-MPI on Rocks cluster- strange results

[Diego Enry Gomes]

These results are not strange.
Performance results really depend on the size/setup of your system.  
Next time use gmxbench so we can have a better reference.


Are you using gromacs 4.0.4 ? It scales much better than gromacs-3.x.x  
versions. Anyway, this very bad scaling is normal over gigabit  
ethernet even with cat6 cables and some tricks like using two network  
interfaces per node. (also two switches or with two VPNs)


If you can't afford an infiniband interfaces there is a solution. You  
can try installing the GAMMA drivers for your ethernet interface and  
MPI/GAMMA as MPI. However I'm not quite sure if GAMMA is stable. Also  
you will need two network interfaces, one of them must be Intel.


http://www.disi.unige.it/project/gamma/mpigamma/index.html


On Mar 6, 2009, at 12:34 AM, kala wrote:

i have ran a particular MD of protein in water for 100ps (50,000  
steps) in a variety of combinations


1. on a single processor( non-mpi) intel core2duo 2.2Ghz 2 GB ram  
time taken : 1hr 30 min
2. 2 processors on a single machine (MPI) similar specs time taken :  
35 min
3 .2 processors on different machines (mpi) similar specs time  
taken : 1hr 5 min
4 .5 processors on 5 different machines (mpi) similar specs time  
taken: 38 min
5.10 processors on 5 different machines(mpi) similar specs time  
taken: 45 min


OS
for 1- open discovery ( fedora 9)
for 2-5 Rocks cluster 5.1

network connectivity Gigabit on cat6
Are the above specified time intervals normal or i am making big big  
mistakes.

comments are invited.
kala bharath
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Re: [gmx-users] Porcupine Plots

[Diego Enry Gomes]

Check the VMD list, you should find the script there.

On Feb 1, 2009, at 9:28 PM, Mark Abraham wrote:


nahren manuel wrote:

Dear Gromacs Users,
I have done PCA of my MD , I want to visually represent the motions  
in terms of porcupine plots. I came across Dynamite (web server)  
for this purpose. But it only considers 500 frames of the xtc file.
Is there any other way how i could generate porcupine plots based  
on tools of GROMACS ?


I've never heard of such plots - perhaps you should look for  
pointers wherever you came across them in the first place?


Users on this list might help with some nuts and bolts, but first  
you need to make sure we can have access to useful information -  
like URLs and algorithm descriptions.


Mark
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Re: [gmx-users] Performance problems with more than one node

[Diego Enry]

Tiago you can try merging two network interfaces with "channel
bonding" it's native on all new (2.6.x) linux kernels. You only need
two network adapters (most dual socket boards come with then), two
network switches ( or two VPN on the same switch).

To tell you the truth, you will not much improvement even with the
latest gromacs version (4beta). However other software that may be
used by your group like NAMD, GAMESS, will benefit a lot from this
approach. (it almost doubles network bandwidth)

The best solution for gromacs is to migrate to infiniband. Go for it,
it is not super expensive anymore.


On Tue, Sep 23, 2008 at 1:48 PM, Jochen Hub <[EMAIL PROTECTED]> wrote:
> Tiago Marques wrote:
>> I don't know how large the system is. I'm the cluster's system administrator
>> and don't understand much of what's going on. The test was given to me by a
>> person who works with it. I can ask him or look at it, if you can point me
>> how to do it.
>
> Hi,
>
> you can count the nr of atoms in the structure:
>
> grep -c ATOM protein.pdb
>
> Jochen
>
>>
>> Thanks, I will look at some of his posts.
>>
>> Best regards,
>>
>> Tiago Marques
>>
>>
>> On Tue, Sep 23, 2008 at 4:03 PM, Jochen Hub <[EMAIL PROTECTED]> wrote:
>> Tiago Marques wrote:
>>> Hi!
>>>
>>> I've been using Gromacs on dual-socket quad-core Xeons with 8GiB of RAM,
>>> connected with Gigabit Ethernet and I always seem to have problems scaling
>>> to more than a node.
>>>
>>> When I run a test on 16 cores, it does run but the result is often slower
>>> than when running on only 8 cores on the same machine. The best result
>> I've
>>> managed is not being slower than 8 cores on 16.
>>>
>>> What am I missing here, or are the tests inappropriate to run over more
>> than
>>> one machine?
>>
>> How large is your system? Which gromacs version are you using?
>>
>> And have a look at the messages by Carsten Kutzner in this list, he
>> wrote a lot on gromacs scaling.
>>
>> Jochen
>>
>>> Best regards,
>>>
>>> Tiago Marques
>>>
>>>
>>>
>>> 
>>>
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>>
>> --
>> 
>> Dr. Jochen Hub
>> Max Planck Institute for Biophysical Chemistry
>> Computational biomolecular dynamics group
>> Am Fassberg 11
>> D-37077 Goettingen, Germany
>> Email: jhub[at]gwdg.de
>> Tel.: +49 (0)551 201-2312
>> 
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>
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> Computational biomolecular dynamics group
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Re: [gmx-users] Bonds missing in VMD visualization

[Diego Enry]

So I was testing on VMD the C-CL bond distance to draw a bond.
Actually, the limit was a disturbing 1.80A ! So close to the 1.81A you
need :(

Solutions !

1) Use "dynamic bonds representation" and set the cut-off to 1.81 or more

2) Find where VMD sets it's standard cutoff for bonds and set it to
1.81 or more forever.

3) VMD FAQ solution is to make a .PSF (topology) to solve this
problem. ( You will only need the bond list )
http://www.ks.uiuc.edu/Research/vmd/allversions/vmd_faq.html

How to write a .PSF file
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node21.html


On Tue, Sep 2, 2008 at 5:59 AM, Andreas Kring <[EMAIL PROTECTED]> wrote:
> Thank you for your reply. I tried the following:
>
>> VMD computes distances between pairs of atoms to "draw" a bond. So I
>> think your atoms are too distanced from each other.
>> Check the bond distribution during MD and compare with your topology.
>> C-CL should be around 1.76A.
>
> In 1,1,1-trichloroethane the C-Cl bond distance should be around 1.81A. I
> checked the C-Cl bond distances using g_bond and this give a nice Gaussian
> distribution around 1.81A (which matches what is in the topology file).
>
>> VMD will not show this bond if, in the REFERENCE frame (the .gro/pdb
>> you open before the .xtc/.trr), this distance is greater than 2.0A.
>
> All bond distances are less than 2.0A, but VMD still does not draw a bond?
>
> Is there anything else I can try?
>
> /Andreas
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-- 
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Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] Bonds missing in VMD visualization

[Diego Enry]

VMD computes distances between pairs of atoms to "draw" a bond. So I
think your atoms are too distanced from each other.
Check the bond distribution during MD and compare with your topology.
C-CL should be around 1.76A.
VMD will not show this bond if, in the REFERENCE frame (the .gro/pdb
you open before the .xtc/.trr), this distance is greater than 2.0A.


On Mon, Sep 1, 2008 at 10:45 AM, Andreas Kring <[EMAIL PROTECTED]> wrote:
> Hello,
>
> I have run an MD simulation of 1000 1,1,1-trichloroethane molecules and it
> all worked nicely. But when I try to visualize the trajectory file in VMD
> some of the C-Cl bonds are missing (although all the atoms appear on the
> screen - only bonds are missing)?
>
> Can I do anything to fix this?
>
> /Andreas
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-- 
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Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] Simulation of silicon oxide surfaces

[Diego Enry]

Hi Michael, look for the bionano tutorial at VMD site. It will
instruct you how to use TCL to build your SiO surface from an "unit
cell".
In a near future they will release the "inorganic builder plugin" that
will make things a LOT easier.

have fun !


On Tue, Jul 15, 2008 at 9:37 AM, Michael Hirtz <[EMAIL PROTECTED]> wrote:
> Hello,
>
> I want to set up a silicon oxide surface with varying -OH surface group for my
> simulation. Does anybody know a tool that could do that or maybe even has a
> topology I could start on and alter manually?
>
> Thanks for any sugesstions,
>Michael
> --
> http://www.defux.de
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-- 
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Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [Bulk] [gmx-users] RMSD graph

[Diego Enry]

Like Yang Ye said, molecule is likely out of the box (just fix PBC).
This also happens when you don't know how to continue a broken
simulation (check the WIKI on gmx website)
I had this PBC issue many times. What works over here to make things easier is:

Be sure that in the reference frame "-s" the molecule is in the box.

1) remove pbc
trjconv -s md.tpr -f md.xtc -o md.nojump.xtc -pbc nojump  (also remove
water since you don't need them for g_rms)

2) check with "vmd" to see if it worked

3) fit the trajectory  ( and keep for animations :) )
trjconv -s md.tpr -f md.nojump.xtc -o md.nojump.fit.xtc -fit rot+trans

4) check the result with "vmd", it looks beautiful

5) g_rms -f  md.nojump.fit.xtc .

Have fun,
Diego Enry.

On Wed, Jun 18, 2008 at 2:55 AM, Yang Ye <[EMAIL PROTECTED]> wrote:
> Quite likely, it is due to part of molecule moving "out of box". Also, the
> molecule could be of multiple chain.
>
> So you need to find a way to put the whole molecule in one piece. Try
> various options from trjconv -pbc. If it is DNA, a trick is to define one
> chain as an index group and then center that group.
>
> Regards,
> Yang Ye
>
> Anamika Awasthi wrote:
>>
>>
>> Dear All,
>>   Please tell, what should I predict from this graph?
>>   I can understand this is normal type of graph.
>>   Sorry for inconvenience, but I want to ask some questions,
>> my this job crashed many time, because of power shut down and I had to
>> restart this again and again, I used tpbconv for the same.
>> but now when I was trying to get rmsd plot from my running job..its not
>> reading the tpr file, which I got from tpbconv , its reading previous tpr
>> file.
>> Is it okey?
>>  Thanks in advance
>> Anamika
>>
>>
>> 
>>
>>
>> 
>>
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] help with gromacs install in opensuse 64b

[Diego Enry]

On Sun, Apr 27, 2008 at 6:49 PM, fabracht sdf <[EMAIL PROTECTED]> wrote:
> I am trying to install gromacs on opensuse 10. I've compiled fftw lybraries
> every possible way i could, but every time i try to install gromacs, i mean,
> every time i run ./configure --enable-mpi i get the same error. I have tryed
> to find the solution to this in the grmx mailing lists but couldn't find the
> exact same error or a solution that suited me. Maybe I should look some
> more, but i someone could give me a help that would be really good. Here is
> the error line the ./configure generates.

did you compile & installed as root ?

I usually get this "checking for main in -lfftw3f... no" when I forget
to compile FFTW with single precision. Try this for fftw:

# single
make distclean
./configure --enable-float --enable-sse --enable-threads --enable-type-prefix
make
make install

# double
make distclean
./configure --enable-sse2 --enable-threads --enable-type-prefix
make
make install

>  ...
> checking for fftw3.h... yes
> checking for main in -lfftw3f... no
> configure: error: Cannot find fftw3f library
> [EMAIL PROTECTED]:~/Download/gromacs-3.3.2>
>
> Thank you in advance.
> Fabrício Bracht
>
>
> ___
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] Help, cannot compile with mpi

[Diego Enry]

./configure can't find "mpicc". If it was really intalled, so the
location of the binaries is not in the variable $PATH.

find where you installed LAM binaries and put it on $PATH

example for bash, type on terminal:
export PATH=$PATH:/usr/local/lam/bin/

You should put this export line on /etc/bash.bashrc so all users won't
need to use the export command (or type the fill path) everytime they
want to use it..



On Sat, Apr 12, 2008 at 2:19 PM, fabracht sdf <[EMAIL PROTECTED]> wrote:
> I've tried to recompile gromacs, this time i tried to enable mpi so tha t i
> can run in parallel. I did what you advised in my last post. I've checked on
> the gromacs homepage, and tried to find instructions for that. Eventually
> what i did was.
>  In the gromacs directory i typed:
> make distclean
>
> and then i wrote the command line described below.
> i says it can't compile and link mpi code with cc.
> lam-mpi is already installed, i would really appreciate some help with this
> problem.
>  Thank you
>
> [EMAIL PROTECTED]:~/Desktop/gromacs-3.3.3#./configure --enable-mpi
>
> checking build system type... i686-pc-linux-gnu
> checking host system type... i686-pc-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
>  checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> checking for gawk... no
> checking for mawk... mawk
> checking whether make sets $(MAKE)... yes
> checking how to create a ustar tar archive... gnutar
>  checking for cc... cc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
>  checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether cc accepts -g... yes
> checking for cc option to accept ISO C89... none needed
> checking for style of include used by make... GNU
>  checking dependency style of cc... gcc3
> checking dependency style of cc... gcc3
> checking for mpxlc... no
> checking for mpicc... no
> checking for mpcc... no
> checking for hcc... no
> checking whether the MPI cc command works... configure: error: Cannot
> compile and link MPI code with cc
>
>
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] how to put two rmsd plot in one plot

[Diego Enry]

You mean 2 plots ? one above the other ? Or all this data on the same plot ?


On Thu, Apr 3, 2008 at 1:27 AM, Mark Abraham <[EMAIL PROTECTED]> wrote:
> Rui Li wrote:
>  > Dear all,
>  > I need two rmsd plots(protein and the ligand) , and I want use one plot 
> display
>  > them, How can I do it?
>
>  Please describe better.
>
>  Mark
>
>
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] restarting MD simulation

[Diego Enry]

Detailed info on gmx wiki
http://wiki.gromacs.org/index.php/Doing_Restarts


On Fri, Mar 28, 2008 at 1:18 PM, David van der Spoel
<[EMAIL PROTECTED]> wrote:
> serdar durdagi wrote:
>  > Dear all,
>  >
>  > I would like to restart a mdrun simulation, which crashed after
>  > a computer shut-down.
>  >
>  > (As structure file, I have only the initial "*.gro" file).
>  >
>  > How can I do this?
>  >
>  tpbconv
>  > Kind Regards,
>  >
>  > Serdar Durdagi
>  >
>  > 
>  > Lesen Sie Ihre E-Mails jetzt einfach von unterwegs mit *Yahoo! Go*
>  > 
> <http://uk.rd.yahoo.com/evt=51524/*http://de.mobile.yahoo.com/interstitial?refer=e00127
>  >  >.
>  >
>  >
>  > 
>  >
>  > ___
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>
>
>  --
>  David.
>  
>  David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>  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
>  [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
>  
>  ___
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] Install on a 64 bit dual core machine - Debian linux

[Diego Enry]

Ricardo, don't worry, it's all the same.

If you deactivate some services like traker (Indexing), bluethooth and
(automatic) graphical environment you may speed up a little your
calculations.


On Wed, Mar 26, 2008 at 7:21 PM, Ricardo Soares <[EMAIL PROTECTED]> wrote:
> Hello gmx users!
>
>  I plan to install gromacs on a 64 bit machine (dual core) runing a
>  debian linux (kubuntu). I've already installed gromacs on other 32 bit
>  machines, and I wonder what are the different steps which I need to take
>  for this particular system. Can anyone give me some insights?
>
>  Thanx in advance.
>
>  --
>  ___
>
>  Ricardo Soares
>  Post-graduation Student in Biological Physics
>  University of Sao Paulo - USP
>  Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
>  Phone: 55 (16) 3602-4840
>  Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
>  ___
>
>  ___
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>  http://www.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] problem with mpi configuration.

[Diego Enry]

/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333
<<= just zoom in the middle of the command

right here:

mpi_d--prefix=

 you forgot to put a space between "mpi_d" and "--prefix"

copy&paste the corrected version bellow.
./configure --enable-mpi --program-suffix=_mpi --prefix=/usr/local/gromacs332

have fun !


On Wed, Mar 12, 2008 at 4:05 PM, mario ciappy <[EMAIL PROTECTED]> wrote:
>
>  Thank you very much for help me.
>  I have try to install gromacs 3.3.3 on rhel 4.0.
>  I try to configure gromacs single with the command  "./configure
> --enable-mpi --program-suffix=_mpi--prefix=/usr/local/gromacs332", but when
> I try to install, I have this error:
>  usr/bin/install: cannot create regular file
> `/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333': No such
> file or directory
>  make[3]: *** [install-binPROGRAMS] Error 1
>  make[3]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
>  make[2]: *** [install-am] Error 2
>  make[2]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
>  make[1]: *** [install-recursive] Error 1
>  make[1]: Leaving directory `/home/mario/gromacs-3.3.3/src'
>  make: *** [install-recursive] Error 1
>  I have try to edit the end of the configure command "/usr/local/gromacs332"
> with"/usr/local/gromacs333" and "/usr/local/gromacs" but I have anlogue
> errors. Can you help me?
>
>  Thanks in advance.
>
>
>  Mario
> Diego Enry <[EMAIL PROTECTED]> ha scritto:
>  You should check the user guide.
> http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs
>
> In a nutshell:
> 1) You need is to install mpich in all machines. Actually you can sync
> the mpich install directory (also gromacs).
> 2) You also need to have the same /etc/hosts on every machine. rsync that.
> 3) You need to grant ssh access without password by creating a rsa-key
> for every user
>
> Fell free to private message if you need any additional help.
>
> Ciao.
>
> On Tue, Mar 4, 2008 at 6:04 AM, mario ciappy wrote:
> > Thank's Diego,
> > I'm grateful to you. I have only one question. How can I configure mpi/lam
> > for relaize the comunication between nodes?
> > I have created an hostsfile with my ip addresses.
> > Thank's a lot in advance.
> >
> > Mario
> >
> > Diego Enry ha scritto:
>
>
> >
> > Since you didn't show us the problems you met.. try following this:
> >
> > #1) Download essential packages
> > #1.1) mpich
> > wget
> >
> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-1.0.6p1.tar.gz
> >
> > #1.2) fftw
> > wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz
> >
> > #1.3) gromacs
> > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz
> >
> >
> > #2) compile packages:
> >
> > #2.1) mpich
> > tar xvfz mpich2-1.0.6p1.tar.gz
> > cd mpich2-1.0.6p1
> > make distclean
> > ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx
> > --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3
> > make
> > make install
> > make distclean
> > cd ..
> >
> > #2.2) fftw single
> > tar xvfz fftw-3.1.2.tar.gz
> > cd fftw-3.1.2
> > make distclean
> > ./configure --enable-float --enable-sse --enable-threads
> > make
> > make install
> > make distclean
> > cd ..
> >
> > #2.3) gromacs single
> > tar xvfz gromacs-3.3.2.tar.gz
> > cd gromacs-3.3.2
> > ./configure --enable-mpi --program-suffix=_mpi
> > --prefix=/usr/local/gromacs332
> > make
> > make install
> > make links
> > make distclean
> > cd ..
> >
> > #2.4) fftw double
> > cd fftw-3.1.2
> > ./configure --enable-sse2 --enable-threads
> > make
> > make install
> > make distclean
> > cd ..
> >
> > #2.2) gromacs double
> > cd gromacs-3.3.2
> > ./configure --enable-mpi --program-suffix=_mpi_d
> > --prefix=/usr/local/gromacs332 --enable-double
> > make
> > make install
> > make links
> > make distclean
> > cd ..
> >
> >
> >
> >
> > On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy wrote:
> > > Dear all,
> > > I'm tried to configure gromacs in parallel but I have meet some
> problems.
> > > I don't understand if the problems are relative to mpi or gromacs
> > > configuration. For this reason I'd be grateful if you explained a
> detailed
> > > installation procedure of all that require to run gromacs

Re: [gmx-users] Gromacs setup on dual core machine

[Diego Enry]

Ricardo, you don't need to uninstall anithing. To run mpi jobs you
only need, mdrun_mpi.

./configure  (with your options)
make mdrun
make install-mdrun

done.

On Tue, Mar 11, 2008 at 1:55 PM, Ricardo Soares <[EMAIL PROTECTED]> wrote:
>
>  Kpiwara De X-nelo wrote:
> Hello
>  You'll need FFTW (fftw.org) LAM/MPI (lam-mpi.org) and gromacs sources
>  Download the 3 packages
>  start with the Lam/MPI (configure , make ,  make install)
>  Then fftw (the 2.1.5 version is needed, the 3.2 supports it but is still
> unstable) (configure --enable-mpi, make, make install)
>  Then, finally, the GROMACS (configure --with-fft=fftw2 --enable-mpi , make
> , make install)
>
>  It should be running
>  as a non root user type lamboot
>  It should start the lam/mpi
>
>  run your simulations as usual just changing these
>  grompp -v -f xx -o xx -c xx -p xx -np #
>
>  the -np generate statusfile for # nodes
>
>  then
>
>  mpirun c0 C mdrun -v -s xx -o xx -e xx -c xx -g x -np # log >& xx
>
>  Number of nodes (#) , must be the same as used for grompp
>
>  the mpirun c0 C tells it to run on the maximun available nodes.
>
>  Hope I helped.
>
>  Matheus Fazian Ige Gondo
>  Departamento de Física e Biofísica
>  Instituto de Biociências
>  Unesp - Botucatu - SP
>  [EMAIL PROTECTED]
>  +55 (14) 3811-6254
>  Hello Matheus, you sure did help!
>  But that way I'd need to uninstall gromacs and reinstall. Is there a way to
> include the LAM/MPI package in an already installed instance of Gromacs? If
> not, how do I uninstal it?
>
>  Thanks again!
>  --
> ___
>
> Ricardo Oliveira dos Santos Soares
> Post-graduation Student in Biological Physics
> University of Sao Paulo - USP
> Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
> Phone: 55 (16) 3602-4840
> Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
> ___
>
> ___
>  gmx-users mailing listgmx-users@gromacs.org
>  http://www.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] Computational efficiency

[Diego Enry]

Ethernet has very high latency, it wasn't made for this kind of thing.
Gmx 4 will be much much better, check the paper gromacs website.


On 3/6/08, Ricardo Soares <[EMAIL PROTECTED]> wrote:
>
>  Diego Enry wrote:
>  On Thu, Mar 6, 2008 at 1:26 PM, Ricardo Soares <[EMAIL PROTECTED]>
> wrote:
>
>
>  Hello everyone,
>
>  I have 3 available computers for my simulations; two of them are dual
>  core. Which is better for me: run one simulation each independently or
>  parallelize them all?
>
>
>  In theory, if the simulations are independent it would be faster to
> run them independently, but you actually doubles the speed if you run
> in parallel in a SINGLE dual core machine.
> I would not recommend you to parallelize it to more than one machine
> if your network fabric is Gigabit Ethernet... unless you are really in
> a hurry to finish a single simulation.
>
> have fun !
>
>
>
>  Thanks!
>
>  Ricardo.
>
>  --
> ___
>
>  Ricardo Oliveira dos Santos Soares
>  Post-graduation Student in Biological Physics
>  University of Sao Paulo - USP
>  Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
>  Phone: 55 (16) 3602-4840
>  Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
> ___
>
>  ___
>  gmx-users mailing list gmx-users@gromacs.org
>  http://www.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at http://www.gromacs.org/search before posting!
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>  www interface or send it to [EMAIL PROTECTED]
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> http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
>
>  Hello Diego,
>
>  Thanks for the tips. Just one more thing, what is the deal with the Gigabit
> Ethernet concerning this topic?
>
>  Regards,
>
>  Ricardo.
>
>  --
> ___
>
> Ricardo Oliveira dos Santos Soares
> Post-graduation Student in Biological Physics
> University of Sao Paulo - USP
> Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
> Phone: 55 (16) 3602-4840
> Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
> ___
>
> ___
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] Computational efficiency

[Diego Enry]

On Thu, Mar 6, 2008 at 1:26 PM, Ricardo Soares <[EMAIL PROTECTED]> wrote:
> Hello everyone,
>
>  I have 3 available computers for my simulations; two of them are dual
>  core. Which is better for me: run one simulation each independently or
>  parallelize them all?
>

In theory, if the simulations are independent it would be faster to
run them independently, but you actually doubles the speed if you run
in parallel in a SINGLE dual core machine.
I would not recommend you to parallelize it to more than one machine
if your network fabric is Gigabit Ethernet... unless you are really in
a hurry to finish a single simulation.

have fun !

>  Thanks!
>
>  Ricardo.
>
>  --
>  ___
>
>  Ricardo Oliveira dos Santos Soares
>  Post-graduation Student in Biological Physics
>  University of Sao Paulo - USP
>  Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
>  Phone: 55 (16) 3602-4840
>  Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
>  ___
>
>  ___
>  gmx-users mailing listgmx-users@gromacs.org
>  http://www.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] problem with mpi configuration.

[Diego Enry]

You should check the user guide.
http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs

In a nutshell:
1) You need is to install mpich in all machines. Actually you can sync
the mpich install directory (also gromacs).
2) You also need to have the same /etc/hosts on every machine. rsync that.
3) You need to grant ssh access without password by creating a rsa-key
for every user

Fell free to private message if you need any additional help.

Ciao.

On Tue, Mar 4, 2008 at 6:04 AM, mario ciappy <[EMAIL PROTECTED]> wrote:
> Thank's Diego,
> I'm grateful to you. I have only one question. How can I  configure mpi/lam
> for relaize the comunication between nodes?
> I have created an hostsfile with my ip addresses.
> Thank's a lot in advance.
>
> Mario
>
> Diego Enry <[EMAIL PROTECTED]> ha scritto:
>
>  Since you didn't show us the problems you met.. try following this:
>
> #1) Download essential packages
> #1.1) mpich
> wget
> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-1.0.6p1.tar.gz
>
> #1.2) fftw
> wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz
>
> #1.3) gromacs
> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz
>
>
> #2) compile packages:
>
> #2.1) mpich
> tar xvfz mpich2-1.0.6p1.tar.gz
> cd mpich2-1.0.6p1
> make distclean
> ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx
> --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3
> make
> make install
> make distclean
> cd ..
>
> #2.2) fftw single
> tar xvfz fftw-3.1.2.tar.gz
> cd fftw-3.1.2
> make distclean
> ./configure --enable-float --enable-sse --enable-threads
> make
> make install
> make distclean
> cd ..
>
> #2.3) gromacs single
> tar xvfz gromacs-3.3.2.tar.gz
> cd gromacs-3.3.2
> ./configure --enable-mpi --program-suffix=_mpi
> --prefix=/usr/local/gromacs332
> make
> make install
> make links
> make distclean
> cd ..
>
> #2.4) fftw double
> cd fftw-3.1.2
> ./configure --enable-sse2 --enable-threads
> make
> make install
> make distclean
> cd ..
>
> #2.2) gromacs double
> cd gromacs-3.3.2
> ./configure --enable-mpi --program-suffix=_mpi_d
> --prefix=/usr/local/gromacs332 --enable-double
> make
> make install
> make links
> make distclean
> cd ..
>
>
>
>
> On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy wrote:
> > Dear all,
> > I'm tried to configure gromacs in parallel but I have meet some problems.
> > I don't understand if the problems are relative to mpi or gromacs
> > configuration. For this reason I'd be grateful if you explained a detailed
> > installation procedure of all that require to run gromacs in parallel,
> > started by mpi/lam configuration. I now that is an hard and demanding
> > request, but it is a big help for me because you are only resource.
> >
> > Thank's in advance
> >
> > Mario
> >
> >
> > 
> > 
> >
> > L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail
> > _______
> > gmx-users mailing list gmx-users@gromacs.org
> > http://www.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 [EMAIL PROTECTED]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Diego Enry B. Gomes
> Laboratório de Modelagem e Dinamica Molecular
> Universidade Federal do Rio de Janeiro - Brasil.
> ___
> gmx-users mailing list gmx-users@gromacs.org
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>
>
>
>  
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> ___
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] problem with mpi configuration.

[Diego Enry]

Since you didn't show us the problems you met.. try following this:

#1) Download essential packages
#1.1) mpich
wget 
http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-1.0.6p1.tar.gz

#1.2) fftw
wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz

#1.3) gromacs
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz


#2) compile packages:

#2.1)  mpich
tar xvfz mpich2-1.0.6p1.tar.gz
cd mpich2-1.0.6p1
make distclean
./configure --with-device=ch3:nemesis --enable-fast --disable-cxx
--enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3
make
make install
make distclean
cd ..

#2.2)  fftw single
tar xvfz fftw-3.1.2.tar.gz
cd fftw-3.1.2
make distclean
./configure --enable-float --enable-sse --enable-threads
make
make install
make distclean
cd ..

#2.3) gromacs single
tar xvfz gromacs-3.3.2.tar.gz
cd gromacs-3.3.2
./configure --enable-mpi --program-suffix=_mpi --prefix=/usr/local/gromacs332
make
make install
make links
make distclean
cd ..

#2.4)  fftw double
cd fftw-3.1.2
./configure --enable-sse2 --enable-threads
make
make install
make distclean
cd ..

#2.2) gromacs double
cd gromacs-3.3.2
./configure --enable-mpi --program-suffix=_mpi_d
--prefix=/usr/local/gromacs332 --enable-double
make
make install
make links
make distclean
cd ..



On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy <[EMAIL PROTECTED]> wrote:
> Dear all,
> I'm tried to configure gromacs in parallel but I have meet some problems.
> I don't understand if the problems are relative to mpi or gromacs
> configuration. For this reason I'd be grateful if you explained a detailed
> installation procedure of all that require to run gromacs in parallel,
> started by mpi/lam configuration. I now that is an hard and demanding
> request, but it is a big help for me because you are only resource.
>
> Thank's in advance
>
> Mario
>
>
>  
> 
>
> L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail
> ___
>  gmx-users mailing listgmx-users@gromacs.org
>  http://www.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 [EMAIL PROTECTED]
>  Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
___
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Re: [gmx-users] Is there any chance to concatenate (fast) more than 1000 energy files....

[Diego Enry]

I think it would take more time to transfer files than doing it on a
single machine, but here is what I suggest:

Assuming you have a cluster of 5 nodes you may concatenate by parts
than put it all together, something like this:

transfer .edr files to /tmp/ of each node than eneconv the fragments
node1 fragments 1-199
node2 fragments 200-399
node3 fragments 400-599
node4 fragments 600-799
node5 fragments 800-1000
transfer all back to your $HOME and eneconv all five fragments.


On Jan 22, 2008 3:56 PM, Sergio <[EMAIL PROTECTED]> wrote:
> Hi all
>
> I'm trying to concatenate more than 1000 energy files, using a bash script
> which runs eneconv program. The problem is that it takes a lot of time to do
> it. Could anyone give me any suggestion of how to improve this task?
>
> Thank you in advance.
>
> --
> Alberto Sergio Garay
> Practica Profesional - Departamente de Física
> Facultad de Bioquímica Y Cs. Biológicas
> Santa Fe - 3000 - Ciudad Universitaria
> Santa Fe - Argentina
>
> ___
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> http://www.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] Gromacs installation: cannot find LibXmu.la

[Diego Enry]

I think I saw this before... check if openmotif contains this library
and install it or just try.

./configure --without-x --enable-mpi

Cheers,
Diego Enry.

On Jan 18, 2008 6:45 AM, Andreas Kukol <[EMAIL PROTECTED]> wrote:
> On SuseLinux 10.3 the command ./configure --enable-mpi works fine but make
> terminates at this point. Using the option --disable-shared did not change 
> anything.
>
> I would be grateful for any help.
>
> Many thanks
> Andreas
>
> Output of make:
> 
> mv -f .deps/nb_free_energy.Tpo .deps/nb_free_energy.Plo
> /bin/sh ../../../libtool --tag=CC   --mode=link mpicc  -O3 -fomit-frame-pointe
>r -finline-functions -Wall -Wno-unused -funroll-all-loops   -o
> libnonbonded.la  nonbonded.lo nb_free_energy.lo
> nb_kernel_x86_64_sse/libnb_kernel_x86_64_sse.la
> nb_kernel/libnb_kernel.la-L/usr/lib64 -lnsl -lfftw3f -lm
> -L/usr/lib64 -lXm -lXt  -lSM -lICE -lX11
> mkdir .libs
> libtool: link: cannot find the library `/usr/lib/libXmu.la' or unhandled argum
>ent `/usr/lib/libXmu.la'
> make[5]: *** [libnonbonded.la] Error 1
> make[5]: Leaving directory `/usr/local/gromacs-3.3.2/src/gmxlib/nonbonded'
> make[4]: *** [all-recursive] Error 1
> make[4]: Leaving directory `/usr/local/gromacs-3.3.2/src/gmxlib/nonbonded'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory `/usr/local/gromacs-3.3.2/src/gmxlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/usr/local/gromacs-3.3.2/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/usr/local/gromacs-3.3.2/src'
> make: *** [all-recursive] Error 1
> --
>
> This is the output of configure:
>
> -
> hecking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking how to create a ustar tar archive... gnutar
> checking for cc... cc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether cc accepts -g... yes
> checking for cc option to accept ISO C89... none needed
> checking for style of include used by make... GNU
> checking dependency style of cc... gcc3
> checking dependency style of cc... gcc3
> checking for mpxlc... no
> checking for mpicc... mpicc
> checking whether the MPI cc command works... yes
> checking how to run the C preprocessor... mpicc -E
> checking whether mpicc accepts -O3... yes
> checking whether mpicc accepts -malign-double... no
> checking whether mpicc accepts -funroll-all-loops... yes
> checking whether mpicc accepts  -O3 -fomit-frame-pointer -finline-functions
> -Wall -Wno-unused -funroll-all-loops... yes
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/bin/grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking whether byte ordering is bigendian... no
> checking for int... yes
> checking size of int... 4
> checking for long int... yes
> checking size of long int... 8
> checking for long long int... yes
> checking size of long long int... 8
> checking floating-point format... IEEE754 (little-endian byte and word order)
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for a sed that does not truncate output... /usr/bin/sed
> checking for ld used by mpicc... /usr/x86_64-suse-linux/bin/ld
> checking if the linker (/usr/x86_64-suse-linux/bin/ld) is GNU ld... yes
> checking for /usr/x86_64-suse-linux/bin/ld option to reload object files... -r
> checking for BSD-compatible nm... /usr/bin/nm -B
> checking how to recognise dependent libraries... pass_all
> checking dlfcn.h usability... yes
> checking dlfcn.h presence... yes
> checking for dlfcn.h... yes
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking dependency style of g++... gcc3

Re: [gmx-users] No scale up beyond 4 processors for 240000 atom system

[Diego Enry]

Low cost tip:
Ask your cluster administrator if it is possible apply channel bonding
to the Gigabit interfaces. You need two network switches for that to
be efficient (a cut-through switch may also help). It increases
network bandwidth by 70%. It also helps to use Cat6 cables.

You may try this MPICH compilation:
./configure --with-device=ch3:nemesis --enable-fast --disable-cxx
--enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3

There is patch to run PME faster over ethernet... maybe that paper
from Dr. Carsten that Dr. Christian suggested.

High cost tip:
Migrate to Infiniband.


Anyone tried GotoBLAS ? Does it work well with GMX ?


On 10/9/07, Christian Burisch <[EMAIL PROTECTED]> wrote:
> Berk Hess schrieb:
>
> Hi all,
>
> > So this is 4 cores sharing one ethernet connection?
>
> perhaps the two Gigabit NICs were bundled somehow. But I guess this
> doesn't work out-of-the-box&plug'n'play. And latency and not bandwidth
> may be limiting in this case.
>
> > With such a setup you will never get good scaling.
> > You need something like an Infiniband network.
>
> Or check:
>
> Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo
> W. Schmitt, Bert L. de Groot and Helmut Grubmuller: Speeding up parallel
> GROMACS on high-latency networks J. Comp. Chem 28 pp. 2075-2084 (2007)
>
> Haven't tried it yet but sounds good!
>
> Regards
>
> Christian
>
> --
> Dr. Christian Burisch
> Lehrstuhl für Biophysik
> PG Theoretische Biophysik
> Ruhr-Universität Bochum
> D-44780 Bochum
> Raum ND04/67
> Fon: +49 234 32 28363
> Fax: +49 234 32 14626
> ___
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] grompp error

[Diego Enry]

ERROR: The cut-off length is longer than half the shortest box vector
or longer than the smallest box diagonal element. Increase the box
size or decrease rlist.

try to "Increase the box size or decrease rlist."  <= as ERROR message suggests




On 10/9/07, pragya chohan <[EMAIL PROTECTED]> wrote:
>
>  hi... i have been trying to do grompp for the following file but am getting
> this error:
>  There were 1 error(s) processing your input
> WARNING 3 [file "popc.top", line 32]:
>   7380 non-matching atom names
>   atom names from popc.top will be used
>   atom names from popc.pdb will be ignored
>  double-checking input for internal consistency...
> ERROR: The cut-off length is longer than half the shortest box vector or
> longer than the smallest box diagonal element. Increase the box size or
> decrease rlist.
> There were 3 warnings
>
>  The grompp command i am using is:
>  grompp -f 7eq_w.mdp -c popc.pdb -p popc.top -o poc.tpr
>
>  the inputs are:
>
>  popc.mdp
>
>  title= popc128a
> integrator   = md
> define   = -DPOSRES -DFLEX_SPC
> dt   = 0.002
> nsteps   = 25000
> nstxout  = 500
> ns_type  = grid
> pbc  = xyz
> constraints  = hbonds
> constraints_algorithm= shake
> coulombtype  = PME
> vdwtype  = cut-off
> rcoloumb = 1.4
>  Tcoupl   = berendsen
> pcoupl   = berendsen
> tau_t= 0.1   0.1
> tc_grps  = POPC  SOL
> ref_t= 300   300
> ref_p= 1.0
> pcoupltype   = isotropic
> compressibility  = 4.5e-5
> gen_temp = 300
>
>  popc.top
>
>  #include "ffgmx.itp"
> #include "lipid.itp"
> #include "popc.itp"
>  #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
>  #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>  ; Include generic topology for ions
> #include "ions.itp"
>  #ifdef POSRES
> #include "lipid_posre.itp"
> #endif
>  [ system ]
> ; Name
> Pure DPPC bilayer with 128 lipids and 3655 water molecules
>  [ molecules ]
> ; Compound#mols
> POPC  128
> SOL   2460
>
>
>
> 
> Call friends with PC-to-PC calling -- FREE Try it now!
> ___
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] restart md from the point it had stopped

[Diego Enry]

[Tsjerk] why do you write velocities and forces every 10 ps?

Third world country my friend, energy supply is not that stable over
here. Also the queue to run a process is huuuge, so every hour is
important. In the end I do a trjconv to reduce # of frames.

Great "Doing Restarts" whoever wrote it :D
http://wiki.gromacs.org/index.php/Doing_Restarts


On 10/9/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
> sarbani chattopadhyay wrote:
> >
> > hi,
> >   I have been running a molecular dynamics simulation for 2
> > nanoseconds.But it stopped in
> > the middle because of an internal problem.Is there any way to restart
> > the simulation from
> > the point it has stopped?
>
> See http://wiki.gromacs.org/index.php/Doing_Restarts for an expanded
> discussion.
>
> Mark
> ___
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> www interface or send it to [EMAIL PROTECTED]
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>


-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] restart md from the point it had stopped

[Diego Enry]

gmxcheck -f broken.trr

check this information:

Item#frames Timestep (ps)
Step   10110
Time   10110
Lambda10110
Coords 10110
Velocities 101  10
Forces   101  10
Box10110

I writing it every 1ps.
I recommend you NOT to use the LAST frame because it may be corrupted
if your simulation was terminated while writing this frame. To
continue, specify the frame just before the last one find above.

tpbconv -s broken.tpr -f broken.trr -e broken.edr -o continue.tpr -time 9

Check If you write velocities&force to the .trr file, I think you
can't get a good continuation without that information.


On 10/8/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
> Hi Sarbani,
>
> Use tpbconv. You can only (properly) restart from a point where you have a
> frame with velocities (in the .trr file) and preferrably energies (.edr).
>
> Best,
>
> Tsjerk
>
>
>  On 8 Oct 2007 12:34:23 -, sarbani chattopadhyay
> <[EMAIL PROTECTED]> wrote:
> >
> >
> >
> >
> > hi,
> >   I have been running a molecular dynamics simulation for 2
> nanoseconds.But it stopped in
> > the middle because of an internal problem.Is there any way to restart the
> simulation from
> > the point it has stopped?
> >
>Thank all
> >
>  Sarbani
> >
> >
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
>  P: +31-30-2539931
> F: +31-30-2537623
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-- 
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Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] restart md from the point it had stopped

[Diego Enry]

Please check the FAQ & list achives b4 posting. Your answer is already there.

Is there any smart way to continue a run that crashed?
http://www.gromacs.org/content/view/62/29/

-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] How to Install GMX V3.3.1 with Intel fortran compiler?

[Diego Enry]

This works for me:

% vim /etc/ld.conf

/opt/intel/mkl/8.0/lib/em64t/   <<<= only if you have installed MKL
/opt/intel/fce/9.0/lib/
/opt/intel/cce/9.0/lib/

then run
% ldconfig


If you wish, you may also add the 32bit libs:
/opt/intel/mkl/8.0/lib/32/  <<<= only if you have installed MKL
/opt/intel/fc/9.0/lib/
/opt/intel/cc/9.0/lib/



On 9/13/07, liu xin <[EMAIL PROTECTED]> wrote:
>
> Dear GMX-users:
>
> I've searched the list but couldnt find something usful for me, and this
> is how I did it so far :
>
> source /opt/intel/fce/version/bin/ifortvars.sh
> export F77=ifort
> export CPPFLAGS=-I/home/xin/programs/fftw312/include
> export LDFLAGS=-L/home/dong/programs/fftw312/lib
> configure --prefix=/home/xin/programs/gromacs331 --enable-fortran
> --enable-mpi
> make mdrun
> make install-mdrun
>
> after the installation, I tried to do the mdrun:
> mpirun -np 2 /home/xin/programs/gromacs331/mdrun -s ...
> and then I got the following error message:
> error while loading shared libraries: libsvml.so: cannot open shared
> object file: No such file or directory
>
> The OS of my pc is SUSE 9.3. And I found that the "missing" file,
> libsvml.so, was in /opt/intel/fce/version/lib
> Is there something wrong with my steps? or shoould I add some FFLAGS?
> I am not very familiar with fortran and Linux, any suggestions will be
> appreciated!
>
> Xin Liu
>
> ___
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] Installation problem on gromacs 3.3.1 during the step make install

[Diego Enry]

-c -m 644 './g_sas.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_sas.1'
> /usr/bin/install: `./g_sas.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_sas.1'
> are the same file
>  /usr/bin/install -c -m 644 './grompp.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/grompp.1'
> /usr/bin/install: `./grompp.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/grompp.1'
> are the same file
>  /usr/bin/install -c -m 644 './x2top.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/x2top.1'
> /usr/bin/install: `./x2top.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/x2top.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_angle.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_angle.1'
> /usr/bin/install: `./g_angle.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_angle.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_dist.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_dist.1'
> /usr/bin/install: `./g_dist.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_dist.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_msd.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_msd.1'
> /usr/bin/install: `./g_msd.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_msd.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_sgangle.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_sgangle.1'
> /usr/bin/install: `./g_sgangle.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_sgangle.1'
> are the same file
>  /usr/bin/install -c -m 644 './highway.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/highway.1'
> /usr/bin/install: `./highway.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/highway.1'
> are the same file
>  /usr/bin/install -c -m 644 './xpm2ps.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/xpm2ps.1'
> /usr/bin/install: `./xpm2ps.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/xpm2ps.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_bond.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_bond.1'
> /usr/bin/install: `./g_bond.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_bond.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_dyndom.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_dyndom.1'
> /usr/bin/install: `./g_dyndom.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_dyndom.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_nmeig.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_nmeig.1'
> /usr/bin/install: `./g_nmeig.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_nmeig.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_sorient.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_sorient.1'
> /usr/bin/install: `./g_sorient.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_sorient.1'
> are the same file
>  /usr/bin/install -c -m 644 './make_ndx.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/make_ndx.1'
> /usr/bin/install: `./make_ndx.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/make_ndx.1'
> are the same file
>  /usr/bin/install -c -m 644 './xrama.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/xrama.1'
> /usr/bin/install: `./xrama.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/xrama.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_bundle.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_bundle.1'
> /usr/bin/install: `./g_bundle.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_bundle.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_enemat.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_enemat.1'
> /usr/bin/install: `./g_enemat.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_enemat.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_nmens.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_nmens.1'
> /usr/bin/install: `./g_nmens.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_nmens.1'
> are the same file
>  /usr/bin/install -c -m 644 './g_tcaf.1' '/people/mail/mariag/gromacs-
> 3.3.1/man/man1/g_tcaf.1'
> /usr/bin/install: `./g_tcaf.1' and 
> `/people/mail/mariag/gromacs-3.3.1/man/man1/g_tcaf.1'
> are the same file
>  /usr/bin/install -c -m 644 '

Re: [gmx-users] ligand topology

[Diego Enry]

On 8/28/07, Blaise Mathias-Costa <[EMAIL PROTECTED]> wrote:
>
>
> hello all,
>
> How to get the topology for a ligand, for which there is no information
> available with the gromacs default libraries!!

Please search the archive at http://www.gromacs.org/search before posting.

A good start would be:
http://wiki.gromacs.org/index.php/PRODRG
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf


>
>
>
> Thanks in advance
>
> Blaise
> ___
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] Error: number of coordinates in coordinate file XXXX.pdb does not match topology (topol.top)

[Diego Enry]

Error: number of coordinates in coordinate file .pdb does not
match topology (topol.top)

Yes, that's really the problem. Check their # of atoms in .pdb and
.top files (count 3xSOL).  You may have used editconf+genbox more than
once. Just start it all over again.

Please remember to search the archive at http://www.gromacs.org/search
before posting.


On 8/28/07, Lycourgos Chiniadis <[EMAIL PROTECTED]> wrote:
> Dear Gromacs users,
>
> I tried the grompp and I got the following message: '' Error: number of
> coordinates in coordinate file .pdb does not match topology
> (topol.top)''.
> Is there any explanation why is this happening?
>
> I would appreciate any help. I am new in using MD and Gromacs in particular.
>
> Thank you in advance,
>
> Best regards,
>
> Lykourgos Chiniadis
> Agricultural University of Athens
> Physics Department
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-- 
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Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] Problem in genion

[Diego Enry]

Hi Ramya,
don't forger to search the archive at http://www.gromacs.org/search
before posting. As David said, it looks like that old genion+
gcc4.series compiler problem. (I also had it) Try compiling with
Intel, gcc-3,gcc-2.96.
Have a nice day.


On 6/6/07, David van der Spoel <[EMAIL PROTECTED]> wrote:

C.RAMYA wrote:
> Hello,
>
>I am facing a problem while trying to neutralize my molecule.
> My molecule is a protein and after writing input file[.tpr] on seeing a
> charge of 6.0e+ i am trying to neutralize it by using 6 CL- ions. when
> i have tried 'genion' for small molecules it was running fine,but for this
> molecule it has been running since 2 days.
> The only message being shown is that only 1 CL- has been introduced.Can
> you please help me out with the necessary steps needed.
> I am actually new to Gromacs,so please help me get through and if possible
> suggest some good material.
>
sounds like a compiler problem that has been fixed. what OS and copiler
are you using?

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se

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--
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] backup files

[Diego Enry]

Pedro, looks like gmx-tools allways want an .extension for input
files, so how about renaming all # files, or at least remove the last
# ?

try this: (quick and dirty)
rename \#conf.gro.1#  #1.conf.gro   \#conf.gro.1#
rename \#conf.tpr.1#   #1.conf.tpr   \#conf.tpr.1#
rename \#conf.edr.1#  #1.conf.edr   \#conf.edr.1#
rename \#conf.xtc.1#  #1.conf.xtc   \#conf.xtc.1#
rename \#conf.trr.1#   #1.conf.trr   \#conf.trr.1#


On 3/17/07, Pedro Alexandre de Araújo Gomes Lapido Loureiro
<[EMAIL PROTECTED]> wrote:

Thank you,

but only for the record, in my system I have to type

cp \#conf.gro#  good.gro
(Note the " \ ")

Regards.

Pedro.

2007/3/17, Mark Abraham <[EMAIL PROTECTED]>:
> > Thanks for you reply but, I'm afraid it doesn't work with me!
> >
> > In fact, if I write "more \#conf.gro#" I can read from this file.
> >
> > However, when using it as input for gromacs utilities the programs
> > complain
> > of input error.
>
> cp #conf.gro# good.gro
>
>
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--
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Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] how to extract frames

[Diego Enry]

Hello Tanos !
check trjconv help,

trjconv -h
-dt   time  0  Only write frame when t MOD dt = first time (ps)

So you may try:
trjconv -s $input.tpr -f $input.xtc -o output.pdb -dt 10


On 2/27/07, Tanos França <[EMAIL PROTECTED]> wrote:

Hi folks,
I can not remember how to procedure to extract frames from the .trr
file after the dynamics simulation. I have performed a MD simulation of
1 ns with a step 0,5 fs and I would like to know how to extract frames
in .pdb files at each 10 ps. Could someone help me with this matter ?
Best regards
Tanos França.

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--
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Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] g_hbond

[Diego Enry]

Maybe not enough memory. Try using "-shell" .


On 12/18/06, Erik Marklund <[EMAIL PROTECTED]> wrote:

On Mon, 2006-12-18 at 13:34 +0200, OZGE ENGIN wrote:
> Hi,
>
> I have a problem with g_hbond. I want to investigate the H bonds formed not only 
within the protein but also between water molecules and the protein.In this respect,  
I select the group 0 --> 'system' option for both selections, an error message 
like the following one appears:
>
> Segmentation fault
>
> How can I fix this problem?

That's hard to say. Which version are you running?

>
> Thanks in advance
>
> Ozge
>
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/Erik

--
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone: +46 18 471 4537  fax: +46 18 511 755
[EMAIL PROTECTED]

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--
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] help Gromacs futil.c error

[Diego Enry]

Diego Enry wrote:
> 4 months later... I´m having the same futil.c File input/output error
> with a brand new instalation. root also works fine for me.



> Hernan how did you solve it ?


On 10/20/06, David van der Spoel <[EMAIL PROTECTED]> wrote:

still the same unix/linux problem. you have to run in your own directory.


Tha was the problem, I was running at "/home/user" folder and still
got the same issue.
Now I realized that "/home" was a very different folder on nodes, so I
removed "/home" on nodes, exported "/home" from server with nfs and
mounted on nodes. Now it is running great !

just for the records
(on server, 192.168.100.0 is the network, 255.255.255.0)
/etc/exports
/home 192.168.100.0/255.255.255.0(rw)

(on nodes, 192.168.100.100 is server IP )
/etc/fstab
192.168.100.100:/home /home nfs rw,addr=192.168.100.100,users 0 0

Thank you guys.


>
>
> On 6/6/06, Mark Abraham <[EMAIL PROTECTED]> wrote:
>> hernan ahumada wrote:
>> > Hello everyone:
>> > I am compiling gromacs 3.3.1 in a X86_64 machine and I have problems
>> >  executing  programs from the gromacs package as normal user. When I
>> > execute the program gives me the following error.
>> >
>> > Program x, VERSION 3.3.1
>> > Source code file: futil.c, line: 308
>> >
>> > File input/output error:
>> > However when I work as root it runs OK.
>> > Please if anybody knows anything about this problems and how to fix it,
>> > I will aknowledge to let me know
>>
>> Probably you are trying to run in a directory in which your normal user
>> doesn't have write access.
>>
>> Also you should post questions to gmx-users only, not also to
>> gmx-users-request.
>>
>> Thanks,
>>
>> Mark
>> ___
>
>


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se

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--
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] help Gromacs futil.c error

[Diego Enry]

4 months later... I´m having the same futil.c File input/output error
with a brand new instalation. root also works fine for me.

Hernan how did you solve it ?


On 6/6/06, Mark Abraham <[EMAIL PROTECTED]> wrote:

hernan ahumada wrote:
> Hello everyone:
> I am compiling gromacs 3.3.1 in a X86_64 machine and I have problems
>  executing  programs from the gromacs package as normal user. When I
> execute the program gives me the following error.
>
> Program x, VERSION 3.3.1
> Source code file: futil.c, line: 308
>
> File input/output error:
> However when I work as root it runs OK.
> Please if anybody knows anything about this problems and how to fix it,
> I will aknowledge to let me know

Probably you are trying to run in a directory in which your normal user
doesn't have write access.

Also you should post questions to gmx-users only, not also to
gmx-users-request.

Thanks,

Mark
_______



--
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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[gmx-users] functionalized surface: counter ions ? PME or RF

[Gomes, Diego Enry B]

Title: functionalized surface: counter ions ? PME or RF






Hello everyone,

I would appreciate some advice on my simulation.

The System is a Protein attached to a small Functionalized Surface

composed of ~250 positive carboxyl groups. The hole system is about

220,000 atoms. (amber,tip3p)


The big concern is how to deal with a net charge of almost "-250" ?

(guide me DNA guys)

1) Should I add a huge amount Na+ as counter ions ? Randomly ?

2) And what about long-range electrostatics ? PME would be fine, or

should I try Reaction-Field ?


Thanks,

--

Diego Enry B. Gomes

@ Pacific Northwest National Laboratory.

Laboratório de Modelagem e Dinamica Molecular

Universidade Federal do Rio de Janeiro - Brasil.



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[gmx-users] functionalized surface: counter ions ? PME or RF.

[Diego Enry]

Hello everyone,
I would appreciate some advice on my simulation.
The System is a Protein attached to a small Funcionalized Surface
composed of ~250 positive carboxyl groups. The hole system is about
220,000 atoms. (amber,tip3p)

The big concern is how to deal with a net charge of almost "-250" ?
(guide me DNA guys)
1) Should I add a huge amount Na+ as counterions ? Randomly ?
2) And what about long-range electrostatics ? PME would be fine, or
should I try Reaction-Field ?

Thanks,
--
Diego Enry B. Gomes
@ Pacific Northwest National Laboratory.
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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Re: [gmx-users] output energies by group

[Diego Enry]

Hi Yuguang,
you don't have to wait your mdrun job to finish to check out your
energies,trajectories.
Just use "g_energy" and you'll get the energies up to the last frame
wrote on .edr file.

Diego Enry.


On 8/4/06, Mu Yuguang (Dr) <[EMAIL PROTECTED]> wrote:

Dear all,
>> How to output energies of different groups during the MD simulation?
>with g_energy, if you have used energy groups in the simulation...

No, I mean output the group energies in the flying ( using cut-off,
during the simulation, not after the simulation), I think I have to
modify the source code.

>
> Best regards
> Yuguang
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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se

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--
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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[gmx-users] g_hbond -g

[Diego Enry]

Hi list,

I couldn't find in the archives and "3.2 to 3.3 changes" what happened
to "-g"  flag in g_hbond ?
Is the old "hbond.log" information written somewhere else ?

Diego Enry.

// command line
g_hbond_331i -g(intel compiled)
// error message:
Program g_hbond_331i, VERSION 3.3.1
Source code file: statutil.c, line: 799

Invalid command line argument:
-g


--
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
[EMAIL PROTECTED]
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