[gmx-users] How to delete bad water molecules

[chris . neale]

I don't know the answer to the exact question that you have posed, but  
I instead suggest that getting rid of that water molecule is not a  
good idea. You should rather minimize your system. While minimizing,  
be sure to include


define=-DFLEXIBLE

in your .mdp file

Try running 500 steps of steep and then 500 steps of l-bfgs, that is  
usually enough for me. Also, be sure to run grompp_d and mdrun_d for  
double precision in the EM portion even if you will use single  
precision for the MD section.


Then remember to NOT include the define=-DFLEXIBLE for the subsequent md run.

Chris.

  Original Message ###

I'm  dealing with a large system of proteins in water molecules of SPC  
model on GMX 3.3.1. When doing position restraints, it always gives  
such error info as follows and then stops:

t = 0.002 ps: Water molecule starting at atom 72750 can not be settled.
Check for bad contacts and/or reduce the timestep.

This error comes from src/mdlib/constr.c:
  if (!bOK && bDumpOnError==1)
	fprintf(stdlog,"\nt = %.3f ps: Water molecule starting at atom %d can  
not be "

"settled.\nCheck for bad contacts and/or reduce the timestep.",
ir->init_t+step*ir->delta_t,owptr[error]+1);

I want to check this naughty guy out and test whether gmx can run  
without this bad water molecule.The question is, there are ~500,000  
atoms in the system and the figure  72750 shows up 5 times. How can I  
know which one is the bad water molecule? Is it the ?72750th  
(?=0,1,2,3,4) atom in the whole system or just in water molecules?


//description of proteins
ATOM  1  N   ALA 1  65.430  66.090  97.040  1.00  0.00
...
//description of water
ATOM  73347  OW  SOL  8016   5.700  12.790  11.830  1.00  0.00
ATOM  73348  HW1 SOL  8016   4.860  12.540  11.310  1.00  0.00
ATOM  73349  HW2 SOL  8016   5.770  13.800  11.860  1.00  0.00
...

Any help would be appreciable.Thank you all in adcance.





Ying  Ren
2007-11-16

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[gmx-users] How to delete bad water molecules

[renying]

I'm  dealing with a large system of proteins in water molecules of SPC model on 
GMX 3.3.1. When doing position restraints, it always gives such error info as 
follows and then stops:
t = 0.002 ps: Water molecule starting at atom 72750 can not be settled.
Check for bad contacts and/or reduce the timestep.

This error comes from src/mdlib/constr.c: 
  if (!bOK && bDumpOnError==1)
fprintf(stdlog,"\nt = %.3f ps: Water molecule starting at atom %d can 
not be "
"settled.\nCheck for bad contacts and/or reduce the timestep.",
ir->init_t+step*ir->delta_t,owptr[error]+1);

I want to check this naughty guy out and test whether gmx can run without this 
bad water molecule.The question is, there are ~500,000 atoms in the system and 
the figure  72750 shows up 5 times. How can I know which one is the bad water 
molecule? Is it the ?72750th (?=0,1,2,3,4) atom in the whole system or just in 
water molecules?

//description of proteins
ATOM  1  N   ALA 1  65.430  66.090  97.040  1.00  0.00
...
//description of water
ATOM  73347  OW  SOL  8016   5.700  12.790  11.830  1.00  0.00
ATOM  73348  HW1 SOL  8016   4.860  12.540  11.310  1.00  0.00
ATOM  73349  HW2 SOL  8016   5.770  13.800  11.860  1.00  0.00
...

Any help would be appreciable.Thank you all in adcance. 





Ying  Ren
2007-11-16


  

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[gmx-users] floating point exception for grompp -e ener.edr on some clusters

[chris . neale]

Hello,

I continue to have difficulties with my newest gromacs compilation  
(3.3.1). The errors that I report here are entirely absent from other  
clusters on which I have compiled gromacs.


The error now is in grompp and looks like this:
Opened sys1800_md689.edr as single precision energy file
Reading frame  0 time 35250.000   Floating point exception  
(core dumped)


Everything works fine if I remove the -e x.edr from the grompp  
command. If I copy all files over to a different cluster and run the  
original command there is no error so this is compilation dependent.


Does anybody have any insight into why I would have this particular  
problem on one installation and not on another?


gmxcheck on the .edr file indicated that it is fine.

Thanks,
Chris.

###

here is the entire output:

$ /scratch/cneale/exe/gromacs-3.3.1/exec/bin/grompp -f  
sys1800_md690.mdp -c sys1800_md689_deshuffleddesorted.gro -t  
sys1800_md689_reshuffleresort.trr -p sys1800.top -n sys1800.ndx  
-deshuf deshuffle_md690.ndx -e sys1800_md689.edr -o sys1800_md690.tpr

 :-)  G  R  O  M  A  C  S  (-:

God Rules Over Mankind, Animals, Cosmos and Such

:-)  VERSION 3.3.1  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

  :-)  /scratch/cneale/exe/gromacs-3.3.1/exec/bin/grompp  (-:

Option Filename  Type Description

  -f sys1800_md690.mdp  Input, Opt!  grompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c sys1800_md689_deshuffleddesorted.gro  InputGeneric structure:
   gro g96 pdb tpr tpb tpa xml
  -r   conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
   xml
 -rb   conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
   xml
  -nsys1800.ndx  Input, Opt!  Index file
-deshufshuffle_md690.ndx  Output, Opt! Index file
  -psys1800.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o sys1800_md690.tpr  Output   Generic run input: tpr tpb tpa xml
  -t sys1800_md689_reshuffleresort.trr  Input, Opt!  Full precision
   trajectory: trr trj
  -e sys1800_md689.edr  Input, Opt!  Generic energy: edr ene

  Option   Type  Value  Description
--
  -[no]h   bool no  Print help info and quit
   -niceint  0  Set the nicelevel
  -[no]v   boolyes  Be loud and noisy
   -time   real -1  Take frame at or first after this time.
 -npint  1  Generate statusfile for # nodes
-[no]shuffle   bool no  Shuffle molecules over nodes
   -[no]sort   bool no  Sort molecules according to X coordinate
-[no]rmvsbds   boolyes  Remove constant bonded interactions with virtual
sites
   -load string Releative load capacity of each node on a
parallel machine. Be sure to use quotes around
the string, which should contain a number for
each node
-maxwarnint 10  Number of warnings after which input processing
stops
-[no]check14   bool no  Remove 1-4 interactions without Van der Waals
  -[no]renum   boolyes  Renumber atomtypes and minimize number of
atomtypes

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
checking input for internal consistency...
calling cpp...
processing topology...
Generated 344865 of the 344865 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 344761 of the 344865 1-4 parameter combinations
Excluding 3 bonded neighbours for DPC 1800
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 224404
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Cleaning up constraints and constant bonded interactions with virtual sites
renumbering atomtypes...
converting bonded parameters...
# ANGLES:   48600
#  PDIHS:   16200
# RBDIHS:   16200
#   LJ14:   46800
# CONSTR:   39600
# SETTLE:   224404
# VSITE3:   224404
Setting particle ty

[gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1 ccc-6.5.6.002-1

[chris . neale]

Find out the c preprocessor of the Compaq C compiler and try to obtain
its output of parsed C source file.


Thanks Yang,

I will give that a shot if I run into any further problems. As it  
turns out it was a problem with our mpicc wrapper. After I localized  
the problem, our sysadmin realized that the string is passing through  
multiple shell layers and getting interpreted. The long-term solution  
is to modify our mpicc script, but for now I have had success  
compiling by doing the following procedure.


MD=/scratch/cneale/exe/gromacs-3.3.1
cd $MD

mkdir exec
export FFTW_LOCATION=/home/cneale/exe/fftw-3.1.2/exec
export GROMACS_LOCATION=${MD}/exec
export CPPFLAGS="-I$FFTW_LOCATION/include"
export LDFLAGS="-L$FFTW_LOCATION/lib"

./configure --prefix=$GROMACS_LOCATION --enable-mpi  
--program-suffix="_mpi" --disable-nice > output.mpi_configure 2>&1

make mdrun > output.mpi_make_mdrun 2>&1

edit src/gmxlib/Makefile and change the line:
AM_CPPFLAGS = -I$(top_srcdir)/include -DGMXLIBDIR=\"$(datadir)/top\"

to:
AM_CPPFLAGS = -I$(top_srcdir)/include -DGMXLIBDIR='\"$(datadir)/top\"'

## note the added single quotes

make mdrun >> output.mpi_make_mdrun 2>&1
make install-mdrun > output.mpi_make_install_mdrun 2>&1

#

Terms to assist future searches:
cc: Error: futil.c, line 516: Invalid expression. (badexpr)
  strcpy(libpath,GMXLIBDIR);
-^
cc: Warning: futil.c, line 516: Invalid token discarded. (invaltoken)
  strcpy(libpath,GMXLIBDIR);
-^

make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed  
by `mdrun'.  Stop.





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Re: [gmx-users] position restrain

[Justin A. Lemkul]

If you read the documentation for genpr, it tells you that it will only generate
a position restraint file for the first molecule, so grompp is telling you that
only the protein is being restrained, which is what you should expect.  If you
really insist on restraining the water molecules, try reading about the
freezegrps options for your .mdp file, but doing so will typically cause
problems if you are using pressure coupling.

-Justin

Quoting pragya chohan <[EMAIL PROTECTED]>:

>
> hi
> I have a system of protein, popc,water and Cl ions. I want to position
> restrain protein and water as without position restrain water is going into
> the membrane . So I made a group of protein and water together using make_ndx
> and then genpr. When i ran grompp i got the following error:
>
> ---
> Program grompp, VERSION 3.3
> Source code file: toppush.c, line: 1108
>
> Fatal error:
> [ file "posre1.itp", line 582 ]:
>  Atom index (5362) in position_restraints out of bounds (1-577)
>
> The commands i used are:
> make_ndx -f em_dpt_popc.gro -o
>  0 System  : 12663 atoms
>   1 Protein :   577 atoms
>   2 Protein-H   :   456 atoms
>   3 C-alpha :59 atoms
>   4 Backbone:   177 atoms
>   5 MainChain   :   237 atoms
>   6 MainChain+Cb:   294 atoms
>   7 MainChain+H :   296 atoms
>   8 SideChain   :   281 atoms
>   9 SideChain-H :   219 atoms
>  10 Prot-Masses :   577 atoms
>  11 Non-Protein : 12086 atoms
>  12 POPC:  4784 atoms
>  13 SOL :  7299 atoms
>  14 Cl  : 3 atoms
>  15 Other   : 12086 atoms
>
>  nr : group   !   'name' nr name   'splitch' nrEnter: list groups
>  'a': atom&   'del' nr 'splitres' nr   'l': list residues
>  't': atom type   |   'keep' nr'splitat' nr'h': help
>  'r': residue 'res' nr 'chain' char
>  "name": group'case': case sensitive   'q': save and quit
>
> > 1|13
>
> Copied index group 1 'Protein'
> Copied index group 13 'SOL'
> Merged two groups with OR: 577 7299 -> 7876
>
>  16 Protein_SOL :  7876 atoms
>
> > q
>
> genpr -f em_dpt_popc.gro -o posre1 -n index.ndx
>
> Group16 ( Protein_SOL) has  7876 elements
> Select a group: 16
> Selected 16: 'Protein_SOL'
>
> grompp -f pr.mdp -c em_dpt_popc.gro -n index.ndx -p dpt_popc_water.top -o
> pr_dpt_popc
>
> What is the best way to do this? Please suggest.
> _
> Check out some new online services at Windows Live Ideas—so new they haven’t
> even been officially released yet.
>
http://www.msnspecials.in/windowslive/___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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> www interface or send it to [EMAIL PROTECTED]
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>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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[gmx-users] position restrain

[pragya chohan]

hi 
I have a system of protein, popc,water and Cl ions. I want to position restrain 
protein and water as without position restrain water is going into the membrane 
. So I made a group of protein and water together using make_ndx and then 
genpr. When i ran grompp i got the following error:

---
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1108

Fatal error:
[ file "posre1.itp", line 582 ]:
 Atom index (5362) in position_restraints out of bounds (1-577)

The commands i used are:
make_ndx -f em_dpt_popc.gro -o
 0 System  : 12663 atoms
  1 Protein :   577 atoms
  2 Protein-H   :   456 atoms
  3 C-alpha :59 atoms
  4 Backbone:   177 atoms
  5 MainChain   :   237 atoms
  6 MainChain+Cb:   294 atoms
  7 MainChain+H :   296 atoms
  8 SideChain   :   281 atoms
  9 SideChain-H :   219 atoms
 10 Prot-Masses :   577 atoms
 11 Non-Protein : 12086 atoms
 12 POPC:  4784 atoms
 13 SOL :  7299 atoms
 14 Cl  : 3 atoms
 15 Other   : 12086 atoms

 nr : group   !   'name' nr name   'splitch' nrEnter: list groups
 'a': atom&   'del' nr 'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr'splitat' nr'h': help
 'r': residue 'res' nr 'chain' char
 "name": group'case': case sensitive   'q': save and quit

> 1|13

Copied index group 1 'Protein'
Copied index group 13 'SOL'
Merged two groups with OR: 577 7299 -> 7876

 16 Protein_SOL :  7876 atoms

> q

genpr -f em_dpt_popc.gro -o posre1 -n index.ndx

Group16 ( Protein_SOL) has  7876 elements
Select a group: 16
Selected 16: 'Protein_SOL'

grompp -f pr.mdp -c em_dpt_popc.gro -n index.ndx -p dpt_popc_water.top -o 
pr_dpt_popc

What is the best way to do this? Please suggest.
_
Check out some new online services at Windows Live Ideas—so new they haven’t 
even been officially released yet.
http://www.msnspecials.in/windowslive/___
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Re: [gmx-users] high pressure simulations

[Andrés N. McCarthy]

Taking up from Mark's comment, you might want to pay special attention to what 
water model you use; i.e. make sure it reproduces some experimentally well 
determined behaviour, such as the "anomalous" autodiffusion coefficient 
maximum (roughly around 2kbar for pure water at 300K).

Cheers.

Andrés


   

On Thu 15 Nov 2007 10:17, Mark Abraham wrote:
> mateusz sikora wrote:
> > Hi all,
> > i am trying to set up high pressure simulations of a protein. I am using
> > NPT ensemble, with isotropic pressure scaling, standard compressibility,
> > room temperature. I am wondering how I can rise pressure from 1 bar to
> > as much as 5 kBar. Is it safe to do it under Parinello-Raman coupling? I
> > want to avoid huge oscillations of a box while adding the pressure -
> > they can result in a box explosion/collapse. Would setting tau_P to some
> > bigger value (like 100 or something) make any difference?
>
> Changing tau_p will damp the extent to which the coupling affects the
> system. You should probably do this process with stepwise increments of
> ref_p. You should also go and parameterize a force field for high
> pressures, too, since the standard ones are parameterized against
> experimental data from 1 bar or so. There's no reason to suppose the
> parameters are transferable to high pressure, unless you can demonstrate
> that they are by comparison of simulation and suitable experimental data.
>
> Mark
> ___
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-- 

Dr. Andrés N. McCarthy
Instituto de Física de Líquidos y Sistemas Biológicos
(UNLP-CONICET-CIC)
Depto. Cs. Biológicas - Fac. de Cs. Exactas - Univ. Nac. de La Plata
59-789, CP (1900) La Plata, Argentina
Tel: +54-221-4254904 / +54-221-4233283
FAX: +54-221-4257317
e-mail:     [EMAIL PROTECTED]
web site:   www.iflysib.unlp.edu.ar
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RE: [gmx-users] Minor Bug in latest stable release update

[Berk Hess]

Ah, forgot to commit that . Done now.

Berk.



From: Maik Goette <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: GMX-mailinglist 
Subject: [gmx-users] Minor Bug in latest stable release update
Date: Thu, 15 Nov 2007 13:35:39 +0100

Hi

I found a missing entry in include/pme.h. Could be connected to the free 
energy/PME problems, Berk recently solved.
In the declaration of spread_on_grid, there's a variable in the function 
missing.


This is how it looks:
extern void spread_on_grid(FILE *logfile,
   t_fftgrid *grid, int homenr,
   int pme_order,   rvec x[],
   real charge[],   matrix box,
   bool bGatherOnly,bool bHaveSplines);

This is how it should:
extern void spread_on_grid(FILE *logfile,
   t_fftgrid *grid,  int homenr,
   int pme_order,rvec x[],
   real charge[],matrix box,
   bool bGatherOnly,
   bool bFreeEnergy, bool bHaveSplines);

Leads to a break while compiling GROMACS

Regards
--
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
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_
Hotmail en Messenger on the move http://www.msn.nl/services

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Re: [gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1

[Yang Ye]

Find out the c preprocessor of the Compaq C compiler and try to obtain 
its output of parsed C source file.


On 11/15/2007 10:12 AM, [EMAIL PROTECTED] wrote:
I have had some success reproducing the event with a simple c program 
and the issue appears to be with the in-house mpicc wrapper script. 
The difference between gcc and mpicc appears limited to strings 
(-D=\"string\") and does not show up in numerical form (e.g. -D=4)


I'll post another update when the issue is resolved.

Chris.

In the following examples cc is the same as mpicc (they both point to 
a script called 'compile') but mpicc invokes slightly different 
linking options than cc


$ cat prog.c
#include 
#include 

int main(int argn,char *args[]){
printf("The value of MYDEF is %s\n",MYDEF);
}

$ gcc prog.c -DMYDEF=\"aaa\" -o prog
$ prog
The value of MYDEF is aaa
$ cc prog.c -DMYDEF=\"aaa\" -o prog
cc: Error: prog.c, line 5: In this statement, "aaa" is not declared. 
(undeclared)

printf("The value of MYDEF is %s\n",MYDEF);
--^

###
However, when the defined value is a number, the problem dissapears:

$ cat prog_num.c
#include 
#include 

int main(int argn,char *args[]){
printf("The value of MYDEF is %d\n",MYDEF);
}

$ gcc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4
$ cc prog_num.c -DMYDEF=4 -o prog_num
$ prog_num
The value of MYDEF is 4

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Re: [gmx-users] high pressure simulations

[Ran Friedman]

Dear Mateusz,

You may be aware of that, but just in case: please note that the
forcefield parameters are usually developed with an ambient pressure in
mind. Both proteins and water change somewhat when a higher pressure is
applied. These changes involve e.g. equilibrium lengths of bonds and the
dielectric of water. Whether or not this has a significant effect on
your simulation depends on what you're actually studying.

As to your question, note that the isotermal compressibility also
changes with the pressure and you'll have to take that into account as
well. Maybe if you change only this parameter and keep tau_P to a value
that works in ambient pressure you'll be fine. You may also try to
increase the pressure gradually and equilibrate.

Ran.

mateusz sikora wrote:
> Hi all,
> i am trying to set up high pressure simulations of a protein. I am
> using NPT ensemble, with isotropic pressure scaling, standard
> compressibility, room temperature. I am wondering how I can rise
> pressure from 1 bar to as much as 5 kBar. Is it safe to do it under
> Parinello-Raman coupling? I want to avoid huge oscillations of a box
> while adding the pressure - they can result in a box
> explosion/collapse. Would setting tau_P to some bigger value (like 100
> or something) make any difference?
> I appreciate any help
> Regards
>
> -- 
> Mateusz Sikora
> http://www.karakorum2008.e-gory.pl
> 
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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-- 
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: [EMAIL PROTECTED]
Skype: ran.friedman
--

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Re: [gmx-users] high pressure simulations

[Andrés N. McCarthy]

Hi Mateusz,
IMHO the berendsen Berendsen barostat is a better option to avoid introducing 
important oscillations in pressure.
For an alternatives on how to proceed with pressure scaling and equilibrating 
you might find useful to read through some of the following recent 
publications on the subject:

Effect of pressure on the conformation of proteins. A molecular dynamics 
simulation of lysozyme 
Journal of Molecular Graphics and Modelling 
Volume 24, Issue 4 , January 2006, Pages 254-261

Pressure denaturation of Apomyoglobin. A molecular dynamics simulation study.
Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics 
Volume 1764, Issue 3 , March 2006, Pages 506-515

Cheers,

Andrés





On Thu 15 Nov 2007 09:48, mateusz sikora wrote:
> Hi all,
> i am trying to set up high pressure simulations of a protein. I am using
> NPT ensemble, with isotropic pressure scaling, standard compressibility,
> room temperature. I am wondering how I can rise pressure from 1 bar to as
> much as 5 kBar. Is it safe to do it under Parinello-Raman coupling? I want
> to avoid huge oscillations of a box while adding the pressure - they can
> result in a box explosion/collapse. Would setting tau_P to some bigger
> value (like 100 or something) make any difference?
> I appreciate any help
> Regards

-- 

Dr. Andrés N. McCarthy
Instituto de Física de Líquidos y Sistemas Biológicos
(UNLP-CONICET-CIC)
Depto. Cs. Biológicas - Fac. de Cs. Exactas - Univ. Nac. de La Plata
59-789, CP (1900) La Plata, Argentina
Tel: +54-221-4254904 / +54-221-4233283
FAX: +54-221-4257317
e-mail:     [EMAIL PROTECTED]
web site:   www.iflysib.unlp.edu.ar
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[gmx-users] Minor Bug in latest stable release update

[Maik Goette]

Hi

I found a missing entry in include/pme.h. Could be connected to the free 
energy/PME problems, Berk recently solved.
In the declaration of spread_on_grid, there's a variable in the function 
missing.


This is how it looks:
extern void spread_on_grid(FILE *logfile,
   t_fftgrid *grid, int homenr,
   int pme_order,   rvec x[],
   real charge[],   matrix box,
   bool bGatherOnly,bool bHaveSplines);

This is how it should:
extern void spread_on_grid(FILE *logfile,
   t_fftgrid *grid,  int homenr,
   int pme_order,rvec x[],
   real charge[],matrix box,
   bool bGatherOnly,
   bool bFreeEnergy, bool bHaveSplines);

Leads to a break while compiling GROMACS

Regards
--
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
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Re: [gmx-users] high pressure simulations

[Mark Abraham]

mateusz sikora wrote:

Hi all,
i am trying to set up high pressure simulations of a protein. I am using 
NPT ensemble, with isotropic pressure scaling, standard compressibility, 
room temperature. I am wondering how I can rise pressure from 1 bar to 
as much as 5 kBar. Is it safe to do it under Parinello-Raman coupling? I 
want to avoid huge oscillations of a box while adding the pressure - 
they can result in a box explosion/collapse. Would setting tau_P to some 
bigger value (like 100 or something) make any difference?


Changing tau_p will damp the extent to which the coupling affects the 
system. You should probably do this process with stepwise increments of 
ref_p. You should also go and parameterize a force field for high 
pressures, too, since the standard ones are parameterized against 
experimental data from 1 bar or so. There's no reason to suppose the 
parameters are transferable to high pressure, unless you can demonstrate 
that they are by comparison of simulation and suitable experimental data.


Mark
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[gmx-users] high pressure simulations

[mateusz sikora]

Hi all,
i am trying to set up high pressure simulations of a protein. I am using NPT
ensemble, with isotropic pressure scaling, standard compressibility, room
temperature. I am wondering how I can rise pressure from 1 bar to as much as
5 kBar. Is it safe to do it under Parinello-Raman coupling? I want to avoid
huge oscillations of a box while adding the pressure - they can result in a
box explosion/collapse. Would setting tau_P to some bigger value (like 100
or something) make any difference?
I appreciate any help
Regards

-- 
Mateusz Sikora
http://www.karakorum2008.e-gory.pl
___
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Re: [gmx-users] compilation fails on MAC OSX - Leopard

[Carsten Kutzner]

Hi Hadas,

I think the problem is that the make command for some reason thinks it
should build the Itanium inner loops:

> ld: in ../gmxlib/.libs/libgmx_mpi.a(nb_kernel204_ia32_sse.o), in

though on your machine the x86_64 kernels should be build. Probably one
can set the correct architecture with a flag to the configure command
like --build=... or --host=...

But I'm not an expert here.

Carsten


Hadas Leonov wrote:
> Hi all,
> 
> I am trying to install Gromacs 3.3.2 on the new Leopard Mac OSX. the OSX
> was installed anew, and not from an upgrade. Developer tools were
> installed too.
> 
> I have already compiled and installed lam-7.0.6 and fftw-3.0.1 (single
> and double precision) without a problem.
> The configure parameters were:
>   
> for lam: ./configure --with-fc=/usr/local/bin/gfortran
> for fftw (single): ./configure --enable-float --enable-threads --enable-sse
> for fftw (double): ./configure --enable-threads --enable-sse2
> 
> 
> For gromacs, the configuration is:  ./configure --enable-mpi
> when I type make, compilation begins and end with the following lines: 
> 
> mpicc -I/sw/include -framework Accelerate -o grompp topio.o toppush.o
> topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o
> vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o
> compute_io.o  -L/usr/local/lib ../mdlib/.libs/libmd_mpi.a -L/usr/X11/lib
> -L/sw/lib ../gmxlib/.libs/libgmx_mpi.a /usr/local/lib/libfftw3f.a -lm
> /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib
> /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib
> /usr/X11/lib/libXdmcp.6.0.0.dylib
> ld: in ../gmxlib/.libs/libgmx_mpi.a(nb_kernel204_ia32_sse.o), in section
> __TEXT,__text reloc 1: bad pc-rel vanilla relocation length
> 
> collect2: ld returned 1 exit status
> make[3]: *** [grompp] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all] Error 2
> make: *** [all-recursive] Error 1
> 
> attached below is configure output for Gromacs. 
> 
> Has anyone else encountered this problem or has any idea how to deal
> with it ?
> 
> Thanks in advance,
> 
> Hadas Leonov. 
> [EMAIL PROTECTED] 
> Department of Biological Chemistry
> Alexander Silberman institute of Life Sciences
> The Hebrew University, 
> Jerusalem, Israel
> 
> 
> 
> 
> checking build system type... i386-apple-darwin9.0.0
> checking host system type... i386-apple-darwin9.0.0
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... config/install-sh -c -d
> checking for gawk... no
> checking for mawk... no
> checking for nawk... no
> checking for awk... awk
> 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... yes
> checking whether mpicc accepts -funroll-all-loops... yes
> **
> * Using CFLAGS from environment variable *
> **
> 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... 4
> 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/libexec/gcc/i686-apple-darwin9/4.0.1/ld
> checking if the linker (/usr/libexec/gcc/i686-apple-

[gmx-users] compilation fails on MAC OSX - Leopard

[Hadas Leonov]

Hi all,I am trying to install Gromacs 3.3.2 on the new Leopard Mac OSX. the OSX was installed anew, and not from an upgrade. Developer tools were installed too.I have already compiled and installed lam-7.0.6 and fftw-3.0.1 (single and double precision) without a problem.The configure parameters were:  for lam: ./configure --with-fc=/usr/local/bin/gfortranfor fftw (single): ./configure --enable-float --enable-threads --enable-ssefor fftw (double): ./configure --enable-threads --enable-sse2For gromacs, the configuration is:  ./configure --enable-mpiwhen I type make, compilation begins and end with the following lines: mpicc -I/sw/include -framework Accelerate -o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o compute_io.o  -L/usr/local/lib ../mdlib/.libs/libmd_mpi.a -L/usr/X11/lib -L/sw/lib ../gmxlib/.libs/libgmx_mpi.a /usr/local/lib/libfftw3f.a -lm /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/libXdmcp.6.0.0.dylibld: in ../gmxlib/.libs/libgmx_mpi.a(nb_kernel204_ia32_sse.o), in section __TEXT,__text reloc 1: bad pc-rel vanilla relocation lengthcollect2: ld returned 1 exit statusmake[3]: *** [grompp] Error 1make[2]: *** [all-recursive] Error 1make[1]: *** [all] Error 2make: *** [all-recursive] Error 1attached below is configure output for Gromacs. Has anyone else encountered this problem or has any idea how to deal with it ?Thanks in advance,Hadas Leonov. [EMAIL PROTECTED]Department of Biological ChemistryAlexander Silberman institute of Life SciencesThe Hebrew University, Jerusalem, Israelchecking build system type... i386-apple-darwin9.0.0
checking host system type... i386-apple-darwin9.0.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
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... yes
checking whether mpicc accepts -funroll-all-loops... yes
**
* Using CFLAGS from environment variable *
**
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... 4
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/libexec/gcc/i686-apple-darwin9/4.0.1/ld
checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) is GNU 
ld... no
checking for /usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld option to reload 
object files... -r
checking for BSD-compatible nm... /usr/bin/nm -p
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
checking how to run the C++ preprocessor... g++ -E
checking the maximum length of command line arguments... 196608
checking command to parse /usr/bin/nm -p output from mpicc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip...

[gmx-users] compilation fails on MAC OSX - Leopard

[Hadas Leonov]

Hi all,I am trying to install Gromacs 3.3.2 on the new Leopard Mac OSX. the OSX was installed anew, and not from an upgrade. Developer tools were installed too.I have already compiled and installed lam-7.0.6 and fftw-3.0.1 (single and double precision) without a problem.The configure parameters were:  for lam: ./configure --with-fc=/usr/local/bin/gfortranfor fftw (single): ./configure --enable-float --enable-threads --enable-ssefor fftw (double): ./configure --enable-threads --enable-sse2For gromacs, the configuration is:  ./configure --enable-mpiwhen I type make, compilation begins and end with the following lines: mpicc -I/sw/include -framework Accelerate -o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o compute_io.o  -L/usr/local/lib ../mdlib/.libs/libmd_mpi.a -L/usr/X11/lib -L/sw/lib ../gmxlib/.libs/libgmx_mpi.a /usr/local/lib/libfftw3f.a -lm /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/libXdmcp.6.0.0.dylibld: in ../gmxlib/.libs/libgmx_mpi.a(nb_kernel204_ia32_sse.o), in section __TEXT,__text reloc 1: bad pc-rel vanilla relocation lengthcollect2: ld returned 1 exit statusmake[3]: *** [grompp] Error 1make[2]: *** [all-recursive] Error 1make[1]: *** [all] Error 2make: *** [all-recursive] Error 1attached below is configure output for Gromacs. Has anyone else encountered this problem or has any idea how to deal with it ?Thanks in advance,Hadas Leonov. [EMAIL PROTECTED]Department of Biological ChemistryAlexander Silberman institute of Life SciencesThe Hebrew University, Jerusalem, Israel checking build system type... i386-apple-darwin9.0.0
checking host system type... i386-apple-darwin9.0.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
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... yes
checking whether mpicc accepts -funroll-all-loops... yes
**
* Using CFLAGS from environment variable *
**
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... 4
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/libexec/gcc/i686-apple-darwin9/4.0.1/ld
checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) is GNU 
ld... no
checking for /usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld option to reload 
object files... -r
checking for BSD-compatible nm... /usr/bin/nm -p
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
checking how to run the C++ preprocessor... g++ -E
checking the maximum length of command line arguments... 196608
checking command to parse /usr/bin/nm -p output from mpicc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip..

Re: [gmx-users] REMD As A Function of Distance Between 2 Chains

[Mark Abraham]

Huey Ling Tan wrote:

Dear all ,
thank you for those comments, we are aware of the paper.  However, we 
are not sure how to implement the replica exchange in gromacs.  We would 
like to run a set of replicas in which each replica corresponds to a 
different set of umbrella parameters.  However, when setting up a 
replica exchange run, all .tpr files use the same .ppa file so that each 
replica will have the same umbrella potential parameters.   Do you know 
how to get around this problem.


You will have to change the code to implement this algorithm.

Mark
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Re: [gmx-users] make gives error in futil.c with mpi and ccc-6.5.6.002-1

[Yang Ye]

Hi,

this post is bit misorganized. so you have passed ./configure stage? I 
tackle the obvious first.


1. On Compaq platform, use export MPICC="gcc 
-L/usr/lib/mpi/mpi_compaq/lib -lmpifarg -lmpi -lelan"
2. it seems that the compiler doesn't receive Macro definition from 
commandline, so you may go into the files to hard code the string values 
(e.g. GMXLIBDIR are present in tools/futil.c and kernel/topio.c)


Regards,
Yang Ye

On 11/15/2007 6:59 AM, Chris Neale wrote:
I am having difficulty installing the mpi version of gromacs 3.3.2 on  
a new computer. I have the same problems for 3.3.1. The serial 
version  appears to have worked fine. The cluster uses elan for MPI I 
have parsed some values from config.log

configure:3291: ccc -V >&5
Compaq C T6.5-002 on Linux 2.4.21-3.7qsnet alpha
Installed as ccc-6.5.6.002-1
Red Hat Linux release 7.2 (Enigma)
Using /usr/lib/gcc-lib/alpha-redhat-linux/2.96 (4).
Compiler Driver T6.5-001 (Linux) cc Driver

I believe my previous post was rejected since it was >2000 lines so I 
have put the
entire config.log here: 
http://www.pomeslab.com/CN_GromacsPost_111407.html

and reposted.

mpicc appears to link like this (although the script is complicated 
enough

that I am not sure if this variable gets modified later):
my %mpilibs ='-L/usr/lib/mpi/mpi_compaq/lib -lmpifarg -lmpi -lelan'

I think that I must have autoconf somewhere since the Makefile was 
created, however:

$automake --version
automake (GNU automake) 1.4-p5
$ autoconf --version
bash: autoconf: command not found

I have found some posts related to futil.c including the following  
potential fix

http://www.gromacs.org/pipermail/gmx-users/2005-January/013806.html
but I didn't understand where the quotes were intended to go and the  
next reply indicates that this is not a good idea in any event.


Another post indicates that I may be required to link it myself and  
avoid the mpicc wrapper. I have tried including the following lines 
in  my compilation script before calling configure


export CC=gcc
export MPICC=gcc
export LIBS="-lmpi"

but configure ends very quickly with the error message:
checking for C compiler default output file name... configure: error:  
C compiler cannot create executables


Thanks for any assistance.
Chris.



I ran it like this:

#!/bin/bash

MD=/scratch/cneale/exe/gromacs-3.3.2
cd $MD

mkdir exec
export FFTW_LOCATION=/home/cneale/exe/fftw-3.1.2/exec
export GROMACS_LOCATION=${MD}/exec
export CPPFLAGS="-I$FFTW_LOCATION/include"
export LDFLAGS="-L$FFTW_LOCATION/lib"

./configure --prefix=$GROMACS_LOCATION --enable-mpi  
--program-suffix="_mpi" --disable-nice > output.mpi_configure 2>&1

make mdrun > output.mpi_make_mdrun 2>&1
make install-mdrun > output.mpi_make_install_mdrun 2>&1
#make distclean



The first error in the 'make mdrun' output is:

source='futil.c' object='futil.lo' libtool=yes \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H  
-I. -I../../src  -I../../include  
-DGMXLIBDIR=\"/scratch/cneale/exe/gromacs-3.3.2/exec/share/top\"  
-I/home/cneale/exe/fftw-3.1.2/exec/include  -std1 -fast -O4 -no_ifo  
-arch ev6 -unroll 2 -fp_reorder -c -o futil.lo futil.c
 mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include  
-DGMXLIBDIR=\"/scratch/cneale/exe/gromacs-3.3.2/exec/share/top\"  
-I/home/cneale/exe/fftw-3.1.2/exec/include -std1 -fast -O4 -no_ifo  
-arch ev6 -unroll 2 -fp_reorder -c futil.c -o futil.o

cc: Error: futil.c, line 521: Invalid expression. (badexpr)
  strcpy(libpath,GMXLIBDIR);
-^
cc: Warning: futil.c, line 521: Invalid token discarded. (invaltoken)
  strcpy(libpath,GMXLIBDIR);
-^
make[2]: *** [futil.lo] Error 1
make[2]: Leaving directory 
`/mnt/scratch/cneale/exe/gromacs-3.3.2/src/gmxlib'

make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory 
`/mnt/scratch/cneale/exe/gromacs-3.3.2/src/gmxlib'




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Re: [gmx-users] REMD As A Function of Distance Between 2 Chains

[chiradip chatterjee]

plz stop mailing me.


- Original Message 
From: Huey Ling Tan <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
Sent: Wednesday, 14 November, 2007 11:23:01 PM
Subject: Re: [gmx-users] REMD As A Function of Distance Between 2 Chains

Dear all ,
thank you for those comments, we are aware of the paper.  However, we are not 
sure how to implement the replica exchange in gromacs.  We would like to run a 
set of replicas in which each replica corresponds to a different set of 
umbrella parameters.  However, when setting up a replica exchange run, all .tpr 
files use the same .ppa file so that each replica will have the same umbrella 
potential parameters.   Do you know how to get around this problem.

Thank you in advance,
Huey Ling 

On 13/11/2007, Marcus Kubitzki <[EMAIL PROTECTED]> wrote:
Hi Huey Ling,

have a look at Y.Sugita et al. J Chem Phys 113, 6042-6051 (2000) for
details on Hamiltonian REMD, especially the correct exchange criterion.
In their paper, they discuss in detail what you want to do, namely

Replica Exchange Umbrella Sampling.

Marcus

Huey Ling Tan wrote:
> Hi all,
>
> Is it feasible to do parallel tempering (replica exchange) as a function
> of distance with umbrella sampling applied?

>
> I can do REMD for a system containing 2 peptide chains as a function as
> temperatures, where I grompp each of the systems at different
> temperatures, and then gather the fullmd.tpr files in one folder with

> the script I want for full md run.
>
> But what if I want to do REMD as a function of distances (for example at
> 0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file),
> at a fixed temperature, with umbrella sampling applied? If this can be

> done, how should I write the script for the full md run so that each of
> the pull.ppa files can recognise the system that it suppose to pull?
>
> If anyone know how this can be done?
>

> Many thanks.
>
> --
> Best regards,
> Huey Ling
>
>
> 
>
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--
Marcus Kubitzki
Max Planck Institute for Biophysical Chemistry
Computational Biomolecular Dynamics Group
Am Fassberg 11
D-37077 Göttingen
Germany
phone: ++49-551-2012312
fax: ++49-551-2012302

Email: mkubitz[at]gwdg.de
www: http://www.mpibpc.mpg.de/groups/de_groot/
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-- 
Best regards,
Huey Ling


-Inline Attachment Follows-

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