Re: [gmx-users] g_angle gets confused by switching default output file names.

[David van der Spoel]

[EMAIL PROTECTED] wrote:

g_angle -ov angaver.xvg :: yields average angle
g_angle -ov angdist.xvg :: yields angle distribution

My Gromacs-3.3 command was:
g_angle -ov x.xvg -type dihedral -f traj.xtc -s topol.tpr -n my.ndx

Easily avoided, just posting a notice.

'
OK, maybe the program is a bit braindead but actually none of the 
gromacs programs checks for double filenames. If you check your 
directory you'll find a backup file #angdist.xvg.1# with the average 
angle as well as angdist.xvg with the distribution. The average is 
written first, then the file is backuped and the distribution is written.



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Dept. of Cell and Molecular Biology, Uppsala University.
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Re: [gmx-users] Water near protein

[Mark Abraham]

Ashutosh Jogalekar wrote:

Hi
I have a protein that I have simulated for 1 ns. I want to observe  the 
variation in the number of water molecules within 2.0 A of the  backbone 
of the protein, as a function of time. So I should be able  to see this 
variation as a graph in xmgrace, with time on the X axis,  and the 
number within 2.0 A on the Y axis. What command could I use  for doing 
this? If not, is there any way that this can be done?


Please read the descriptions of the utility programs in the gromacs 
manual. If one of those sounds like it does the job, go ahead and try 
it. Otherwise, look around at other tools (I don't know of any, others 
on here might), or write your own.


Mark
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[gmx-users] g_angle gets confused by switching default output file names.

[chris . neale]

g_angle -ov angaver.xvg :: yields average angle
g_angle -ov angdist.xvg :: yields angle distribution

My Gromacs-3.3 command was:
g_angle -ov x.xvg -type dihedral -f traj.xtc -s topol.tpr -n my.ndx

Easily avoided, just posting a notice.
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Re: [gmx-users] Water near protein

[X.Periole]

On Tue, 9 May 2006 16:48:43 -0500
 Ashutosh Jogalekar <[EMAIL PROTECTED]> wrote:

Hi
I have a protein that I have simulated for 1 ns. I want 
to observe  the variation in the number of water 
molecules within 2.0 A of the  backbone of the protein, 
as a function of time. So I should be able  to see this 
variation as a graph in xmgrace, with time on the X axis, 
and the number within 2.0 A on the Y axis. What command 
could I use  for doing this? If not, is there any way 
that this can be done?




g_mindist can counts the number of contacts between two
groups (protine and oxygen of water molecules in your 
case)

within a given distance.

check g_mindist -h

XAvier
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[gmx-users] Water near protein

[Ashutosh Jogalekar]

Hi
I have a protein that I have simulated for 1 ns. I want to observe  
the variation in the number of water molecules within 2.0 A of the  
backbone of the protein, as a function of time. So I should be able  
to see this variation as a graph in xmgrace, with time on the X axis,  
and the number within 2.0 A on the Y axis. What command could I use  
for doing this? If not, is there any way that this can be done?

Thanks very much
Ashutosh Jogalekar

Modeling Laboratory
Chemistry Department
Emory University

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Re: [gmx-users] Segmentation fault in "disco"

[David van der Spoel]

Fabrizio Mancinelli wrote:

Hi all,
I tried to perform a CONCOORD simulation by means of "cdist" and "disco" 
routines included in GROMACS. However, while cdist appears to work well,
disco produces a "segmentation fault" error. Maybe a problem in managing 
memory? Does anybody give me a clue? Thanks in advance!


These programs have been deprecated. Please use the versions by Bert de 
Groot.


--
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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[gmx-users] Segmentation fault in "disco"

[Fabrizio Mancinelli]

Hi all,
I tried to perform a CONCOORD simulation by means of "cdist" and "disco" 
routines included in GROMACS. However, while cdist appears to work well,
disco produces a "segmentation fault" error. Maybe a problem in managing 
memory? Does anybody give me a clue? Thanks in advance!

-- 
Fabrizio Mancinelli, PhD
Dept. Biochemistry and Biophysics
II University of Naples
Naples - Italy
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Re: [gmx-users] Fatal error: moleculetype SOL is redefined.

[Mark Abraham]

Absalom Zamorano wrote:

Strangely enough, the problem is here:


Fatal error:
moleculetype SOL is redefined


Find where moleculetype SOL is defined in your .top file - perhaps 
implicitly through an #include - and you should see it defined more than 
once. Evidently you can't do this :-)


Mark
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Re: [gmx-users] Value for bonded force constant (Kb)

[Mark Abraham]

raja wrote:

Dear gmxions,
   Could any one give me the value for bonded force constant (Kb) to
   be used for restraining ,F(II) and ligating atoms of 
proteins ( 2 HISs and 1 ASP)using harmonic potential (type 6).


Find a paper that does a similar thing and base your construction on 
that and your judgement.


Mark
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[gmx-users] Fatal error: moleculetype SOL is redefined.

[Absalom Zamorano]

Hi gromaxers, I want to generate a tpr file for a
minimization. I have 3 peptides in water and Im using
OPLS ff, but after I run grompp, system backs me the
next message:
--
creating statusfile for 1 node...
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter
combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter
combinations
Excluding 3 bonded neighbours for Protein_X 1
Cleaning up temporary file gromppDDYIem
---
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 887
 
Fatal error:
moleculetype SOL is redefined
--
Some commentary will be very appreciated. 
Thank you for advance.

Dr. Absalom Zamorano Carrillo 
Profesor Titular A 
Programa Institucional de Biomedicina Molecular, ENMyH-IPN
Guillermo Massieu  Helguera  #239 Fracc. "La Escalera"
Ticomán, D.F. México, C.P  07320
Tel. (55) 57296000,  ext 55542







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[gmx-users] Fatal error: moleculetype SOL is redefined.

[Absalom Zamorano]

Hi gromaxers, I want to generate a tpr file for a
minimization. I have 3 peptides in water and Im using
OPLS ff, but after I run grompp, system backs me the
next message:
--
creating statusfile for 1 node...
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter
combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter
combinations
Excluding 3 bonded neighbours for Protein_X 1
Cleaning up temporary file gromppDDYIem
---
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 887
 
Fatal error:
moleculetype SOL is redefined
--
Some commentary will be very appreciated. 
Thank you for advance.

Dr. Absalom Zamorano Carrillo 
Profesor Titular A 
Programa Institucional de Biomedicina Molecular, ENMyH-IPN
Guillermo Massieu  Helguera  #239 Fracc. "La Escalera"
Ticomán, D.F. México, C.P  07320
Tel. (55) 57296000,  ext 55542







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[gmx-users] grompp error on nanotube

[Aina Quintillá]

-- 
Aina Quintillá
Institut fuer Nanotechnologie   
Forschungszentrum Karlsruhe

Tel: +49 (0) 7247 82 6360


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Re: [gmx-users] Speptide - mdrun failed

[David van der Spoel]

[EMAIL PROTECTED] wrote:

Dear All,

I'm just getting started with GROMACS. I configured and installed 
fftw-3.0.1 and then I configured, compiled and installed 
gromacs-3.3.1.tar.gz as INSTALL file showed.
I thought that the installation had been successful and I performed the 
simulation of the peptide (speptide, the one the example proposed).


I executed:

1) pdb2gmx -f speptide.pdb -p speptide.top -o speptide.gro

2) editconf -f speptide -o -d 0.5

3) genbox -cp out -cs -p speptide -o b4em

4) grompp -v -f em.mdp -c b4em -o em -p speptide

Theses steps didn't give me apparent problems. But when I executed:

mdrun -v -s em -o em -c after_em -g emlog

This message appeared:

mdadm: /dev/md-v not identified in config file.


that's another mdrun, to do with the OS.

Try to do the following to start with:
source /path/to/GMXRC
(the file is usually in the bin directory of you installation)



I don't understand what it means. I would appreciate some suggestions to 
continue the example. I am not able to find the answer about it.


Thank you for your help in advance.

Montserrat




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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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[gmx-users] Value for bonded force constant (Kb)

[raja]

Dear gmxions,
   Could any one give me the value for bonded force constant (Kb) to
   be used for restraining ,F(II) and ligating atoms of 
proteins ( 2 HISs and 1 ASP)using harmonic potential (type 6).

With thanks!
B.Nataraj
-- 
  raja
  [EMAIL PROTECTED]

-- 
http://www.fastmail.fm - Faster than the air-speed velocity of an
  unladen european swallow

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Re: [gmx-users] problem with profiling grompp using callgrind

[Berk Hess]

From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] problem with profiling grompp using callgrind
Date: Tue, 09 May 2006 09:36:36 +0200

Berk Hess wrote:




this seems more like a bug that is dependent on memory allocation. I'm no 
aware of any known bug in grompp. Maybe you can recompile all of grompp 
with the -g flag and retry. For memory debugging simpler tools like 
Electric Fence usually work. For profiling, you'd probably want to 
profile mdrun, although there is a bugzilla about grompp being 
excessively slow for large systems with OPLS and dummies.


grompp with OPLS is excessively slow in general, because it generates
LJ parameters for all ~1000^2 atom type combinations.
If you have little memory it will start swapping to disk.


the real problem is in the dummy code, I've done some profiling and there 
are quite a few nested loops there. It's a low priority bug as far as I'm 
concerned, but it's in bugzilla so it will get fixed some time.


That looks like a more serious problem.

But the LJ parameter calculation is also annoying.
I have some free-energy simulations where each OPLS atom type
has an zero LJ equivalent so the LJ matrix is ~2000^2.
grompp allocates 600 MB and my machine with 1 GB of physical memory
and several tasks gets unworkable for several minutes.
I just tested before sending this mail and grompp actually crashed
as it could not allocate enough memory.
Generating the 1-4 parameters seems to take the most time,
probably this causes the most memory access.
On a machine with more memory or less tasks the same system
runs through grompp in a few seconds.

Berk.


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[gmx-users] Speptide - mdrun failed

[montserrat.vaque]

Dear All,



I'm just getting started with GROMACS. I configured and installed
fftw-3.0.1 and then I configured, compiled and installed
gromacs-3.3.1.tar.gz as INSTALL file showed.

I thought that the installation had been successful and I performed the
simulation of the peptide (speptide, the one the example proposed).



I executed:



1) pdb2gmx -f speptide.pdb -p speptide.top -o speptide.gro



2) editconf -f speptide -o -d 0.5



3) genbox -cp out -cs -p speptide -o b4em



4) grompp -v -f em.mdp -c b4em -o em -p speptide



Theses steps didn't give me apparent problems. But when I executed:



mdrun -v -s em -o em -c after_em -g emlog



This message appeared:



mdadm: /dev/md-v not identified in config file.





I don't understand what it means. I would appreciate some suggestions
to continue the example. I am not able to find the answer about it.



Thank you for your help in advance.


Montserrat
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Re: [gmx-users] problem with profiling grompp using callgrind

[David van der Spoel]

Berk Hess wrote:




this seems more like a bug that is dependent on memory allocation. I'm 
no aware of any known bug in grompp. Maybe you can recompile all of 
grompp with the -g flag and retry. For memory debugging simpler tools 
like Electric Fence usually work. For profiling, you'd probably want 
to profile mdrun, although there is a bugzilla about grompp being 
excessively slow for large systems with OPLS and dummies.


grompp with OPLS is excessively slow in general, because it generates
LJ parameters for all ~1000^2 atom type combinations.
If you have little memory it will start swapping to disk.


the real problem is in the dummy code, I've done some profiling and 
there are quite a few nested loops there. It's a low priority bug as far 
as I'm concerned, but it's in bugzilla so it will get fixed some time.






Berk.


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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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Re: [gmx-users] problem with profiling grompp using callgrind

[Berk Hess]

this seems more like a bug that is dependent on memory allocation. I'm no 
aware of any known bug in grompp. Maybe you can recompile all of grompp 
with the -g flag and retry. For memory debugging simpler tools like 
Electric Fence usually work. For profiling, you'd probably want to profile 
mdrun, although there is a bugzilla about grompp being excessively slow for 
large systems with OPLS and dummies.


grompp with OPLS is excessively slow in general, because it generates
LJ parameters for all ~1000^2 atom type combinations.
If you have little memory it will start swapping to disk.

Berk.


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Re: [gmx-users] failed dependencies

[Florian Haberl]

On Monday 08 May 2006 21:00, David van der Spoel wrote:
> Jayant James Jayasundar wrote:
> > hi !
> > I am trying to install GMX on a opteron 2xdual core processor. OS- Suse
> > Linux10.0. I actually installed the intel fortran compiler as I was just
> > not able to get the Suse fortran compiler. I downloaded the suse 10 from
> > opensuse.org.
> > I  get this message while trying to install lam
> > error: Failed dependencies:
> > gcc-g77 is needed by lam-7.0.6-5
> > openssh-clients is needed by lam-7.0.6-5
> > openssh-server is needed by lam-7.0.6-5
> > Suggestions to overcome this problem will be greatly appreciated.
> > Thanks
> > Jayant
>
> disable fortran. you don't need it for gromacs.

To install other packages you need to start yast as root user, and install 
missing packages.
Take a look at http://opensuse.org/

>
> > Jayasundar Jayant James
> > Postdoctoral research fellow,
> > Department of Veterinary and Comparative Anatomy, Pharmacology
> > and Physiology(VCAPP), Washington state university, Pullman
> > 99164-6520, USA.
> > http://www.chick.com/reading/tracts/0001/0001_01.asp
> > Phone office:335-5937, Cell:1-509-432-5790
> >
> >  >gnature-home.htm/[EMAIL PROTECTED]>
> >
> >
> >
> > 
> >
> > ___
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greetings,

Florian

-- 
---
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 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
---
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