Re: [gmx-users] genion - hangs up

[Tsjerk Wassenaar]

Hi Luciane,


 David van der Spoel has replied saying:
 there is a problem compiling gromacs using gcc 4.x that may cause this. see
a recent bugzilla entry about it.


Did you compile using the 4.x gcc? In that case, recompile with an
older version (3.x). That solution was suggested in the same
discussion.


 While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na
and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I
thought it might be my system, so went to /tutor/speptide, but it was the
same behaviour. I am using gromacs 3.3.1. As I recall genion worked fine
under 3.2.


I've had this problem, but only with very high salinity. My solution
to that problem (decreasing the allowed minimal distance between ions)
is likely not going to work for you.v So I'd try recompiling if indeed
you used the 4.x gcc version.


 I am wondering if this problem has already been fixed for version 3.3.1 and
if a update for that is available.
 Is the only solution go back to 3.2?


Frankly, we'd say the problem is with gcc, not with gromacs :) The gcc
team should really fix what they've broken in the 4.x series :p

Cheers,

Tsjerk

--
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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[gmx-users] GAMESS-US for Hybrid QM/MM

[Srivastava, Dhiraj (UMC-Student)]

Hi All

   Is there any way to use gamess-us for Hybrid QM/MM calculation with 
Gromacs instead of using CPMD, GAMESS-uk or gaussion? 

Thanks

Dhiraj

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Re: [gmx-users] mdrun -rerun problems

[George Abadir]

Yes of course I looked at the output but I thought is I specify energy 
groups it will output only those specified and not the whole system. 
However I tried a short run and it did output both. For the crash it 
turned out it is because all the nodes try to read the huge trajectory 
file at the same time if this may help somebody in the future. We are 
still trying to figure out how to solve this problem anyway.

Thanks for your time.
George

Mark Abraham wrote:


George Abadir wrote:


Hi all,
I am running simulations of carbon nanotubes and amino acids 
in water. I need to calculate the potential energies for the whole 
system as well as the interaction energy between the CNT  and amino 
acid. What I am tried to do is to calculate the energy for the whole 
system first (i.e. I did not introduce any energygrps in the run.mdp 
file) and then use the rerun option to calculate the interaction 
energy after introducing "energygrps= CNT Protein SOL" into the 
run.mdp file. However, each time I try to run this second step the 
cluster on which I run the simulation crashes with a message "Kernel 
panicked"!

Does any body know about this problem?



Yeah, something's broken that's probably got nothing to do with 
GROMACS, or the fact you're doing a re-run.


Is there another way to get both the potential energy of the system 
as well as the interaction potential energy? I understand that if I 
write "energygrps= CNT Protein SOL" from the very beginning the 
energy of the whole system won't be written, is that right?



mdrun always calculates the total potential and kinetic energy, and 
outputs it according to nstxxx flags.

Have you not looked at typical output, or typical .edr file contents?

Mark
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Re: [gmx-users] mdrun -rerun problems

[Mark Abraham]

George Abadir wrote:

Hi all,
I am running simulations of carbon nanotubes and amino acids in 
water. I need to calculate the potential energies for the whole system 
as well as the interaction energy between the CNT  and amino acid. What 
I am tried to do is to calculate the energy for the whole system first 
(i.e. I did not introduce any energygrps in the run.mdp file) and then 
use the rerun option to calculate the interaction energy after 
introducing "energygrps= CNT Protein SOL" into the run.mdp file. 
However, each time I try to run this second step the cluster on which I 
run the simulation crashes with a message "Kernel panicked"!

Does any body know about this problem?


Yeah, something's broken that's probably got nothing to do with GROMACS, 
or the fact you're doing a re-run.


Is there another way to get both 
the potential energy of the system as well as the interaction potential 
energy? I understand that if I write "energygrps= CNT Protein SOL" from 
the very beginning the energy of the whole system won't be written, is 
that right?


mdrun always calculates the total potential and kinetic energy, and 
outputs it according to nstxxx flags.

Have you not looked at typical output, or typical .edr file contents?

Mark
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Re: [gmx-users] mdp file help

[Mark Abraham]

Probably, you've broken your line endings transferring to/from a Windows 
machine.


Mark
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Re: [gmx-users] Implicit solvent simulation

[Eric Jakobsson]

There is a niche for implicit solvent if you need to do more 
extensive conformational sampling than you can achieve with 
atomically detailed solvent---and if you can plausibly argue that you 
are not introducing such egregious systematic errors that you are 
just sampling more junk.


At 09:23 AM 7/18/2007, TJ Piggot wrote:
If you REALLY want implicit solvent then i suggest you contact the 
authors and ask them about it, however i (like most others i think) 
have never needed to use implicit solvent.


Tom

--On Wednesday, July 18, 2007 16:17:01 +0200 Ran Friedman 
<[EMAIL PROTECTED]> wrote:



Dear Tom,

The paper is available and was mentioned in the list. The model,
however, isn't available AFAIK.

Ran.

TJ Piggot wrote:

Hi,

Just to let people know in case they are unaware there is a paper
where implicit solvent models have been implemented in GROMACS, the
paper can be found using the following link:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid
=15814616


Tom

--On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel
<[EMAIL PROTECTED]> wrote:


SeungPyo Hong wrote:

Thank you for your kind reply, Stephane.
Anyhow it is a little disappointing that Generalized-Born is not
implemented in Gromacs.


I've put it on the development TODO list (feel free to volunteer)

http://wiki.gromacs.org/index.php/Implicit_Solvent

The reason it is not there is because none of the developers has
considered it worthwhile.

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax:
+4618511755.
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
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University of Bristol, UK.

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--
--
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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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-
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry, and of the Center for Biophysics and Computational Biology

Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
3261 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896  Fax 217 244 9757




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[gmx-users] Re: Install problem

[Ibrahim M. Moustafa]

h Alan, but the
>> challengefor us isn't to write a trivial Still GB implementation, but
>> to make it perform well. There's little point in having a GB
>> implementation that is slower than the fast explicit-solvent
>> simulations in Gromacs!
>>
>>
>
> Happy to hear that, if you need some 
beta-tester for validation and performance

> tests, i'm your man :-)
>
You can help already now, by heading over to
http://wiki.gromacs.org/index.php/Implicit_Solvent
and adding more documentation.

Although I realize it is the holiday season, at least in Europe, I would
like to once more recommend the development wiki for documenting this
kind of discussion, and for publishing specifications for algorithms,
like (totally unrelated, but came up earlier today):
http://wiki.gromacs.org/index.php/Cpp_replacement

Cheers,
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se


--

Message: 3
Date: Wed, 18 Jul 2007 16:20:41 -0400
From: John Mercer <[EMAIL PROTECTED]>
Subject: [gmx-users] install problem
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Hi,

I am a beginning user of GROMACS, and am just now trying to get a
functional installation.  There is something not quite right about
the installations I have tried.  I have spent considerable time
testing ideas about what might be the problem, but have not nailed
it.  I am hoping someone will have a suggestion (perhaps obvious)
that will reduce the time I am spending getting GROMACS operational.
I can duplicate the problem with multiple GROMACS subprograms but
will only refer to "luck" (luck.c).

Platform:  Mac OS X 10.4.10

Installations tried:
1. Binary package install of 
gromacs-3.3.dmg.gz (from www.gromacs.org)

2. Fink with compile; first standalone, then remove standalone and
install openmpi
In both cases, GMXRC.bash is sourced in "profile".
3. All installations exhibit the same problem so I'll stick to fink.

Indications:
1. luck -c executes with a segmentation fault from any directory.
2. /sw/bin/luck -c executes normally 
from any directory. (/usr/local/

bin installation exhibits same problem.)
3. Not a UNIX PATH problem as non GROMACS functions in /sw/bin
execute normally from the same shell.
4. A shorter PATH value does function normally without regard to
where fink subdirectories are placed in the PATH, causing me to
wonder whether PATH is parsed in code with a fixed memory variable.


Diagnostics:
1. luck -c prints the GROMACS banner before it's segmentation fault
2. /sw/bin/luck -c prints the banner, a wording for the GROMACS
acronym, a version number, the authors, software information, and a
user friendly quote.
3. Comparing 1. & 2. with luck.c, 
copyrite.c, etc suggestions that a

call to bromacs() in CopyRight() migh be where the problem manifests
itself.
4. The call sequence could be CopyRight() -> bromacs() -> pukeit() -
 > low_lib_libopen() -> low_libfn().
5. Note: I haven't tested all these functions to verify they are
each involved, but suggest them as a hypothesis based on the output
and looking at traces of system calls.
6. One thing that puzzles me is that it looks as if low_libfn()
expects "GMXLIB" as an environment variable, but the script
GMXRC.bash sets up "GMXLDLIB as the library environment variable.

Whatever the problem, the program executes from any directory, but
only with the full path specified does it execute without a
segmentation fault.


Any advice on how to fix this problem would be greatly appreciated.

John Mercer


--

Message: 4
Date: Wed, 18 Jul 2007 16:50:22 -0400
From: "srinivas aripirala" <[EMAIL PROTECTED]>
Subject: [gmx-users] How to include Mg in the input file?
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"

Skipped content of type 
multipart/alternative-- next part --

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Name: GME_final.inp
Type: application/octet-stream
Size: 7224 bytes
Desc: not available
Url : 
http://www.gromacs.org/pipermail/gmx-users/attachments/20070718/c0a6ed0c/GME_final.obj

-- next part --
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--

_

Re: [gmx-users] How to include Mg in the input file?

[David van der Spoel]

srinivas aripirala wrote:

Hello everybody,

I am attaching both the pdb and the inp. while i was trying to run the 
inp file.

It errors our saying the Mg (magnesium )

  ERROR  PCM SPHERE(S) MUST HAVE A POSITIVE RADIUS

Guys when i diagonize i see that there it has included radius for MG as 0.

has anybody come across this problem earlier?



you're not even saying what you want to do, but it looks like QM/MM.
you should probably read up on your QM code whatever it is that does not 
support Mg.




Thanks in advance
Srinivas




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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] install problem

[David van der Spoel]

John Mercer wrote:

Hi,

I am a beginning user of GROMACS, and am just now trying to get a 
functional installation.  There is something not quite right about the 
installations I have tried.  I have spent considerable time testing 
ideas about what might be the problem, but have not nailed it.  I am 
hoping someone will have a suggestion (perhaps obvious) that will reduce 
the time I am spending getting GROMACS operational.  I can duplicate the 
problem with multiple GROMACS subprograms but will only refer to "luck" 
(luck.c).


Platform:  Mac OS X 10.4.10

Installations tried:
1. Binary package install of gromacs-3.3.dmg.gz (from www.gromacs.org)
2. Fink with compile; first standalone, then remove standalone and 
install openmpi

In both cases, GMXRC.bash is sourced in "profile".
3. All installations exhibit the same problem so I'll stick to fink.

Indications:

1. luck -c executes with a segmentation fault from any directory.
2. /sw/bin/luck -c executes normally from any directory. 
(/usr/local/bin installation exhibits same problem.)
3. Not a UNIX PATH problem as non GROMACS functions in /sw/bin 
execute normally from the same shell.
4. A shorter PATH value does function normally without regard to 
where fink subdirectories are placed in the PATH, causing me to wonder 
whether PATH is parsed in code with a fixed memory variable.



Diagnostics:
1. luck -c prints the GROMACS banner before it's segmentation fault
2. /sw/bin/luck -c prints the banner, a wording for the GROMACS 
acronym, a version number, the authors, software information, and a user 
friendly quote.
3. Comparing 1. & 2. with luck.c, copyrite.c, etc suggestions that a 
call to bromacs() in CopyRight() migh be where the problem manifests 
itself.
4. The call sequence could be CopyRight() -> bromacs() -> pukeit() 
-> low_lib_libopen() -> low_libfn().
5. Note: I haven't tested all these functions to verify they are 
each involved, but suggest them as a hypothesis based on the output and 
looking at traces of system calls.
6. One thing that puzzles me is that it looks as if low_libfn() 
expects "GMXLIB" as an environment variable, but the script GMXRC.bash 
sets up "GMXLDLIB as the library environment variable.


Whatever the problem, the program executes from any directory, but only 
with the full path specified does it execute without a segmentation fault.



Any advice on how to fix this problem would be greatly appreciated.


have you tried using csh?
csh
source .../bin/GMXRC

just guessing at this point, but on my mac it works fins under a 
c-shell, an always has.


--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] How to include Mg in the input file?

[srinivas aripirala]

Hello everybody,

I am attaching both the pdb and the inp. while i was trying to run the inp
file.
It errors our saying the Mg (magnesium )

 ERROR  PCM SPHERE(S) MUST HAVE A POSITIVE RADIUS

Guys when i diagonize i see that there it has included radius for MG as 0.

has anybody come across this problem earlier?

Thanks in advance
Srinivas


GME_final.inp
Description: Binary data


GME_final.pdb
Description: Protein Databank data
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[gmx-users] install problem

[John Mercer]

Hi,

I am a beginning user of GROMACS, and am just now trying to get a  
functional installation.  There is something not quite right about  
the installations I have tried.  I have spent considerable time  
testing ideas about what might be the problem, but have not nailed  
it.  I am hoping someone will have a suggestion (perhaps obvious)  
that will reduce the time I am spending getting GROMACS operational.   
I can duplicate the problem with multiple GROMACS subprograms but  
will only refer to "luck" (luck.c).


Platform:  Mac OS X 10.4.10

Installations tried:
1. Binary package install of gromacs-3.3.dmg.gz (from www.gromacs.org)
	2. Fink with compile; first standalone, then remove standalone and  
install openmpi

In both cases, GMXRC.bash is sourced in "profile".
3. All installations exhibit the same problem so I'll stick to fink.

Indications:
1. luck -c executes with a segmentation fault from any directory.
	2. /sw/bin/luck -c executes normally from any directory. (/usr/local/ 
bin installation exhibits same problem.)
	3. Not a UNIX PATH problem as non GROMACS functions in /sw/bin  
execute normally from the same shell.
	4. A shorter PATH value does function normally without regard to  
where fink subdirectories are placed in the PATH, causing me to  
wonder whether PATH is parsed in code with a fixed memory variable.



Diagnostics:
1. luck -c prints the GROMACS banner before it's segmentation fault
	2. /sw/bin/luck -c prints the banner, a wording for the GROMACS  
acronym, a version number, the authors, software information, and a  
user friendly quote.
	3. Comparing 1. & 2. with luck.c, copyrite.c, etc suggestions that a  
call to bromacs() in CopyRight() migh be where the problem manifests  
itself.
	4. The call sequence could be CopyRight() -> bromacs() -> pukeit() - 
> low_lib_libopen() -> low_libfn().
	5. Note: I haven't tested all these functions to verify they are  
each involved, but suggest them as a hypothesis based on the output  
and looking at traces of system calls.
	6. One thing that puzzles me is that it looks as if low_libfn()  
expects "GMXLIB" as an environment variable, but the script  
GMXRC.bash sets up "GMXLDLIB as the library environment variable.


Whatever the problem, the program executes from any directory, but  
only with the full path specified does it execute without a  
segmentation fault.



Any advice on how to fix this problem would be greatly appreciated.

John Mercer
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Re: [gmx-users] Implicit solvent simulation

[David van der Spoel]

[EMAIL PROTECTED] wrote:

Selon Erik Lindahl <[EMAIL PROTECTED]>:


Hi,

On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:


The version used by Alan Mark has never made it into gromacs.
Rather, Erik Lindahl started the implementation of this stuff but
did never finish it completely, due to other priorities I presume.
We should however take out the variables to avoid confusion (unless
someone provides a full implementation).

Actually, technically the GB implementation is already in Gromacs
(even assembly kernels), and quite correct, it's just that you don't
have the born radii yet :-)

The last couple of years we've mainly done membrane stuff where it's
not useful for my students, and thus not a priority to implement.
However, recently Per Larsson has finished C implementations of the
Still radius calculations that I've started optimizing.

The big remaining task is the SA part of GB/SA, i.e. the surface
calculation, which also needs to be optimized and preferrably
parallelized (harder) to be useful.



Erik, didn't you say once that you implemented fast area calculations 
and derivatives?


It's an interesting CS problem, but there certainly are at least a 
couple of papers on these topics.


Fan Hao actually offered us the code he wrote with Alan, but the
challengefor us isn't to write a trivial Still GB implementation, but
to make it perform well. There's little point in having a GB
implementation that is slower than the fast explicit-solvent
simulations in Gromacs!




Happy to hear that, if you need some beta-tester for validation and performance
tests, i'm your man :-)

You can help already now, by heading over to 
http://wiki.gromacs.org/index.php/Implicit_Solvent

and adding more documentation.

Although I realize it is the holiday season, at least in Europe, I would 
like to once more recommend the development wiki for documenting this 
kind of discussion, and for publishing specifications for algorithms, 
like (totally unrelated, but came up earlier today):

http://wiki.gromacs.org/index.php/Cpp_replacement

Cheers,
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] Implicit solvent simulation

[steletch]

Selon Erik Lindahl <[EMAIL PROTECTED]>:

> Hi,
>
> On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
>
> > The version used by Alan Mark has never made it into gromacs.
> > Rather, Erik Lindahl started the implementation of this stuff but
> > did never finish it completely, due to other priorities I presume.
> > We should however take out the variables to avoid confusion (unless
> > someone provides a full implementation).
>
> Actually, technically the GB implementation is already in Gromacs
> (even assembly kernels), and quite correct, it's just that you don't
> have the born radii yet :-)
>
> The last couple of years we've mainly done membrane stuff where it's
> not useful for my students, and thus not a priority to implement.
> However, recently Per Larsson has finished C implementations of the
> Still radius calculations that I've started optimizing.
>
> The big remaining task is the SA part of GB/SA, i.e. the surface
> calculation, which also needs to be optimized and preferrably
> parallelized (harder) to be useful.
>
>
> Fan Hao actually offered us the code he wrote with Alan, but the
> challengefor us isn't to write a trivial Still GB implementation, but
> to make it perform well. There's little point in having a GB
> implementation that is slower than the fast explicit-solvent
> simulations in Gromacs!
>
>

Happy to hear that, if you need some beta-tester for validation and performance
tests, i'm your man :-)

Cheers,

Stéphane Téletchéa

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Re: [gmx-users] uniform dielectric constant

[David van der Spoel]

Mikael Lund wrote:
Reading the mailing list and the wiki as well, I see that GROMACS has 
little support for implicit solvent. However, I'm interested in 
simulating charged polymers (small spheres connected with springs) in an 
aqueos salt solution (more spheres). Assuming no dielectric boundaries 
-- i.e. a uniform dielectric continuum -- I thought of setting epsilon_r 
to 80. Clearly the dynamics will be wrong but I'm interested in static 
properties only. Do you see any pitfalls with this approach?


if the potentials are optimized for this it may work, but you probably 
want to read recent polymer literature. Berk Hess has two relevant 
papers in 2006 (one PRL, one JCP) that are done predominantly with GROMACS.

Best,
  Mikael

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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] uniform dielectric constant

[Mikael Lund]

Reading the mailing list and the wiki as well, I see that GROMACS has  
little support for implicit solvent. However, I'm interested in  
simulating charged polymers (small spheres connected with springs) in  
an aqueos salt solution (more spheres). Assuming no dielectric  
boundaries -- i.e. a uniform dielectric continuum -- I thought of  
setting epsilon_r to 80. Clearly the dynamics will be wrong but I'm  
interested in static properties only. Do you see any pitfalls with  
this approach?


Best,
  Mikael

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Re: [gmx-users] Re: Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run (Jim Kress)

[Erik Lindahl]

Hi Jim,

That system should scale quite well with a fast network (infiniband)  
since you don't seem to be using PME, and the CVS 3.99 version is  
even better.


However, as David already mentioned, the gigabit network is likely  
limiting you. If you test the CVS code there are timing reports that  
will tell you how much _time_ (vs. floating-point operations) is  
spent on each part of the algorithm.


Cheers,

Erik



On Jul 18, 2007, at 6:23 PM, Jim Kress wrote:

It's a 3.712 cube containing 1722 tip4p water molecules at 300 deg  
K and

density = 1000kg/l

Regards,

Jim Kress

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Re: [gmx-users] Implicit solvent simulation

[Erik Lindahl]

Hi,

On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:

The version used by Alan Mark has never made it into gromacs.  
Rather, Erik Lindahl started the implementation of this stuff but  
did never finish it completely, due to other priorities I presume.  
We should however take out the variables to avoid confusion (unless  
someone provides a full implementation).


Actually, technically the GB implementation is already in Gromacs  
(even assembly kernels), and quite correct, it's just that you don't  
have the born radii yet :-)


The last couple of years we've mainly done membrane stuff where it's  
not useful for my students, and thus not a priority to implement.  
However, recently Per Larsson has finished C implementations of the  
Still radius calculations that I've started optimizing.


The big remaining task is the SA part of GB/SA, i.e. the surface  
calculation, which also needs to be optimized and preferrably  
parallelized (harder) to be useful.



Fan Hao actually offered us the code he wrote with Alan, but the  
challengefor us isn't to write a trivial Still GB implementation, but  
to make it perform well. There's little point in having a GB  
implementation that is slower than the fast explicit-solvent  
simulations in Gromacs!



Cheers,

Erik







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[gmx-users] Re: Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run (Jim Kress)

[Jim Kress]

It's a 3.712 cube containing 1722 tip4p water molecules at 300 deg K and
density = 1000kg/l

Regards,

Jim Kress

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Re: [gmx-users] Implicit solvent simulation

[David van der Spoel]

Stéphane Téletchéa wrote:

Moore, Jonathan (J) a écrit :

I asked for and received the code a couple of years ago.

As the paper indicates, it's in an ancient version of GROMACS...which
creates challenges.  Also, the different models (Still, etc.) are
implemented in independent versions of the code.  Also, the GB part is
actually implemented in FORTRAN.  


Jonathan



You are lucky, i did so and never got the code.
This raises the question about GPL violations and publication 
trustworthy, since it is published, can we consider the code has been 
made publicly available since provided once a paper has been published, 
we are supposed to be able to reproduce the published work.


I had not pushed a lot for getting the code but since traces are 'still' 
in gromacs code (in every mdp-generated file at least, there is a 
mention about GB parameters), it would be nice to have an official 
statement on this from the core developpers of GROMACS.


I'm not trying to get any grief here, if you consider this a non-issue, 
please ignore the message, that'll be enough to me.


Cheers,
Stéphane

The version used by Alan Mark has never made it into gromacs. Rather, 
Erik Lindahl started the implementation of this stuff but did never 
finish it completely, due to other priorities I presume. We should 
however take out the variables to avoid confusion (unless someone 
provides a full implementation).


--
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] Implicit solvent simulation

[Stéphane Téletchéa]

Moore, Jonathan (J) a écrit :

I asked for and received the code a couple of years ago.

As the paper indicates, it's in an ancient version of GROMACS...which
creates challenges.  Also, the different models (Still, etc.) are
implemented in independent versions of the code.  Also, the GB part is
actually implemented in FORTRAN.   



Jonathan



You are lucky, i did so and never got the code.
This raises the question about GPL violations and publication 
trustworthy, since it is published, can we consider the code has been 
made publicly available since provided once a paper has been published, 
we are supposed to be able to reproduce the published work.


I had not pushed a lot for getting the code but since traces are 'still' 
in gromacs code (in every mdp-generated file at least, there is a 
mention about GB parameters), it would be nice to have an official 
statement on this from the core developpers of GROMACS.


I'm not trying to get any grief here, if you consider this a non-issue, 
please ignore the message, that'll be enough to me.


Cheers,
Stéphane

--
Stéphane Téletchéa, PhD.  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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[gmx-users] genion - hangs up

[Rigden, LucianeVMello]

 
Dear all,

I am having problem with genion.
I have already search the gmx archive, and got the following message:

While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and 
it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it 
might be my system, so went to /tutor/speptide, but it was the same behaviour. 
I am using gromacs 3.3.1. As I recall genion worked fine under 3.2.

I am wondering if this problem has already been fixed for version 3.3.1 and if 
a update for that is available.
Is the only solution go back to 3.2?

David van der Spoel has replied saying:
there is a problem compiling gromacs using gcc 4.x that may cause this. see a 
recent bugzilla entry about it.

any further help on that?


Many thanks in advance,
Luciane

Dr Luciane Vieira de Mello
School of Biological Sciences 
Room 2.20, Life Science Building
Tel:(+44) 151 795 5140
FAX:(+44) 151 794 5130
University of Liverpool
Crown St.,Liverpool L69 7ZB, U.K.

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Re: [gmx-users] mdp file help

[james zhang]

You can get a typical mdp file from some tutorials.
By the way, I think the topology is wrong.
Thanks.


On 7/18/07, Christopher Stiles <[EMAIL PROTECTED]> wrote:


 I am trying to simulate a single wall CNT in a box filled with water for
about 500 ps and 300K just to start and I am having trouble with the mdp
file, basicly what should and should not be in it. I just want it generic to
start and tune it up later. Here is what I have done so far along with links
to copys of the files I have used:




*



Must have the following files in the working directory to start:

SWNT_6_6_144.pdb

Can find a copy at: http://cs86.com/CNSE/SWNT_6_6_144.pdb



ffgmx.n2t

 must change this files name to ffG43b1.n2t and add the following 2
lines:

C   C   1   C   ; CNT Carbon with
one bond

C   C   2   C   C   ; CNT double
bonded Carbon



ffgmxbon.itp

add the following line to it:

CC1   0.14210 478900.





*** you can find copies of both of these files at the following location:

/usr/local/gromacs/share/gromacs/top/



x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp

Note: for some reason it does not generate SWNT_6_6_144.rtp*



editconf -f SWNT_6_6_144.gro -o SWNT_6_6_144.gro  -d 0.5



genbox -cp SWNT_6_6_144.gro  -cs -o SWNT_6_6_144_b4em.gro -p
SWNT_6_6_144.top -maxsol 300

* *

grompp -f em3.mdp -r SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top -o -maxwarn
310




***



 em3.mdp###  Can find a copy at: http://cs86.com/CNSE/em3.mdp



title= SWNT_6_6_144

cpp  = cpp

include  = /usr/local/gromacs/share/gromacs/top/

define   = -DFLEX_SPC

integrator   = md

dt   = 0.002

nsteps   = 50

nstxout  = 5000

nstvout  = 5000

nstlog   = 5000

nstenergy= 250

nstxtcout= 250

xtc_grps = Protein

energygrps   = Protein  SOL

nstlist  = 10

ns_type  = grid

rlist= 0.8

coulombtype  = cut-off

rcoulomb = 1.4

rvdw = 0.8

tcoupl   = Berendsen

tc-grps  = Protein  SOL

tau_t= 0.1  0.1

ref_t= 300  300

Pcoupl   = Berendsen

tau_p= 1.0

compressibility  = 4.5e-5

ref_p= 1.0

gen_vel  = yes

gen_temp = 300

gen_seed = 173529

constraints  = all-bonds



**



This is what I get after running grommp:







-bash-3.00$ grompp -f em3.mdp -r SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top
-o -maxwarn 310

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

.

.

.



  -[no]renum   boolyes  Renumber atomtypes and minimize number of

atomtypes



creating statusfile for 1 node...

' for variable integrator, using 'md'

Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'

' for variable ns-type, using 'Grid'

Next time use one of: 'Grid' 'Simple'

' for variable coulombtype, using 'Cut-off'

Next time use one of: 'Cut-off' 'Reaction-Field'
'Generalized-Reaction-Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift'
'User' 'Generalized-Born' 'Reaction-Field-nec' 'Encad-shift' 'PME-User'

' for variable tcoupl, using 'No'

Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'

' for variable Pcoupl, using 'No'

Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'

' for variable gen-vel, using 'no'

Next time use one of: 'no' 'yes'

' for variable constraints, using 'none'

Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'



Back Off! I just backed up mdout.mdp to ./#mdout.mdp.15#

checking input for internal consistency...

...ling cpp

: command not found

cpp exit code: 32512

 SWNT_6_6_144.top > gromppOpff2m'cs/top -DFLEX_SPC

' command is defined in the .mdp file

processing topology...

processing coordinates...

---

Program grompp, VERSION 3.3.1

Source code file: futil.c, line: 340



File input/output error:

conf.gro

---



"This May Come As a Shock" (F. Black)






***





Any help or advice is greatly appreciated!



~Christopher Stiles

College of Nanoscale Science and Engineering (CNSE)

State University of New York, Albany, New Y

RE: [gmx-users] Implicit solvent simulation

[Moore, Jonathan (J)]

I asked for and received the code a couple of years ago.

As the paper indicates, it's in an ancient version of GROMACS...which
creates challenges.  Also, the different models (Still, etc.) are
implemented in independent versions of the code.  Also, the GB part is
actually implemented in FORTRAN.   


Jonathan


Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
Core R&D
The Dow Chemical Company
1702 Building, Office 300E
Midland, MI 48674  USA
Phone:  (989) 636-9765 
Fax: (989) 636-4019
E Mail: [EMAIL PROTECTED]

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Ran Friedman
Sent: Wednesday, July 18, 2007 10:17 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Implicit solvent simulation

Dear Tom,

The paper is available and was mentioned in the list. The model,
however, isn't available AFAIK.

Ran.

TJ Piggot wrote:
> Hi,
>
> Just to let people know in case they are unaware there is a paper
> where implicit solvent models have been implemented in GROMACS, the
> paper can be found using the following link:
>
>
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid
=15814616
>
>
> Tom
>
> --On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel
> <[EMAIL PROTECTED]> wrote:
>
>> SeungPyo Hong wrote:
>>> Thank you for your kind reply, Stephane.
>>> Anyhow it is a little disappointing that Generalized-Born is not
>>> implemented in Gromacs.
>>>
>>
>> I've put it on the development TODO list (feel free to volunteer)
>>
>> http://wiki.gromacs.org/index.php/Implicit_Solvent
>>
>> The reason it is not there is because none of the developers has
>> considered it worthwhile.
>>
>> -- 
>> David van der Spoel, Ph.D.
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
>> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax:
>> +4618511755.
>> [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
>> ___
>> 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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>> interface or send it to [EMAIL PROTECTED]
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> --
> TJ Piggot
> [EMAIL PROTECTED]
> University of Bristol, UK.
>
> ___
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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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[gmx-users] ACE group parameter error un ffG53a5-6?

[Mauricio Pablo Sica]

Dear all

Sorry for repeating this message. I have found what appears to be an 
error in the files ffG53a(5 and 6).rtp related to the ACE group topology. 
Maybe it is a trivial error, or a change due to something I am missing. 
I’m sure you experts will ponder it much better than me.

I was constructing the topology for N-acetylgalactosamine using the 
parameters for ffG53a5. In general, my strategy was to acetylate a 2-
amino galactose. So, considering the parameters from ffG53a6bon.itp, the 
acetyl group bonded to the NH of the sugar was:

[ bonds ]
  CA  C   gb_27
  C   O   gb_5
  C   N   gb_10 ; this is the parameter for the peptide (amide) bond.

In particular, for the C-N bond, I choose gb_10 according to its 
definition in ffG53a6bon.itp:

 #define gb_10   0.1330  1.1800e+07
 ; C, CR1  -  N, NR, CR1, C (peptide, 5-ring)   1000

The problem arose when I wanted to compare what I did to what is 
parameterized for ACE group in the ffG53a6.rtp. There I found that:

[ bonds ]
  CCA   gb_27
  C O   gb_5
  C+N   gb_19 (Here is the discrepancy)

According to ffG53a6bon.itp, gb_19 defines parameters for C-O bonds, as 
you can see:

 #define gb_19   0.1430  9.2100e+06
 ; CHn  -  OM900 

Could it be an error or the choice is due to something I am missing?

Additionally, in the force fields 43a1, 43a2, 43b1 and 45a3, the 
parameters for the said C-N bonds are gb_9, which is in all cases defined 
as:

 define gb_90.1330  1.1800e+07
 ; C, CR1  -  N, NR, CR1, C (peptide, 5-ring)   1000

Also, in ffG53a6.rtp, "C +N" bonds are paremeterized according to gb_10 
for all residues except for ACE, which has one of the three gb_19 in the 
file (although I know that these statistics are not sufficient for 
dismiss the choice for gb_19).
The question, again, is: is gb_19 correct? If yes, please tell me why.


Sorry for the length of the mail and thanks for your attention.




Dr. Mauricio P. SicaLEPP
Phone: (54011)4365-7100 ext. 169Laboratorio de Expresión
R. Saenz Peña 354   y Plegado Proteico
(B1876BXF) Bernal, Buenos Aires Universidad de Quilmes
Argentina




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Re: [gmx-users] Implicit solvent simulation

[TJ Piggot]

If you REALLY want implicit solvent then i suggest you contact the authors 
and ask them about it, however i (like most others i think) have never 
needed to use implicit solvent.


Tom

--On Wednesday, July 18, 2007 16:17:01 +0200 Ran Friedman 
<[EMAIL PROTECTED]> wrote:



Dear Tom,

The paper is available and was mentioned in the list. The model,
however, isn't available AFAIK.

Ran.

TJ Piggot wrote:

Hi,

Just to let people know in case they are unaware there is a paper
where implicit solvent models have been implemented in GROMACS, the
paper can be found using the following link:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid
=15814616


Tom

--On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel
<[EMAIL PROTECTED]> wrote:


SeungPyo Hong wrote:

Thank you for your kind reply, Stephane.
Anyhow it is a little disappointing that Generalized-Born is not
implemented in Gromacs.



I've put it on the development TODO list (feel free to volunteer)

http://wiki.gromacs.org/index.php/Implicit_Solvent

The reason it is not there is because none of the developers has
considered it worthwhile.

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax:
+4618511755.
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
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[EMAIL PROTECTED]
University of Bristol, UK.

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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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--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.

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Re: [gmx-users] Implicit solvent simulation

[Ran Friedman]

Dear Tom,

The paper is available and was mentioned in the list. The model,
however, isn't available AFAIK.

Ran.

TJ Piggot wrote:
> Hi,
>
> Just to let people know in case they are unaware there is a paper
> where implicit solvent models have been implemented in GROMACS, the
> paper can be found using the following link:
>
> http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15814616
>
>
> Tom
>
> --On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel
> <[EMAIL PROTECTED]> wrote:
>
>> SeungPyo Hong wrote:
>>> Thank you for your kind reply, Stephane.
>>> Anyhow it is a little disappointing that Generalized-Born is not
>>> implemented in Gromacs.
>>>
>>
>> I've put it on the development TODO list (feel free to volunteer)
>>
>> http://wiki.gromacs.org/index.php/Implicit_Solvent
>>
>> The reason it is not there is because none of the developers has
>> considered it worthwhile.
>>
>> -- 
>> David van der Spoel, Ph.D.
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax:
>> +4618511755.
>> [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
>> ___
>> 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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>> interface or send it to [EMAIL PROTECTED]
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>
>
>
> --
> TJ Piggot
> [EMAIL PROTECTED]
> University of Bristol, UK.
>
> ___
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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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[gmx-users] mdp file help

[Christopher Stiles]

I am trying to simulate a single wall CNT in a box filled with water for
about 500 ps and 300K just to start and I am having trouble with the mdp
file, basicly what should and should not be in it. I just want it generic to
start and tune it up later. Here is what I have done so far along with links
to copys of the files I have used:

 


*

 

Must have the following files in the working directory to start:

SWNT_6_6_144.pdb

Can find a copy at: http://cs86.com/CNSE/SWNT_6_6_144.pdb

 

ffgmx.n2t

 must change this files name to ffG43b1.n2t and add the following 2
lines:

C   C   1   C   ; CNT Carbon with
one bond

C   C   2   C   C   ; CNT double bonded
Carbon

 

ffgmxbon.itp

add the following line to it:

CC1   0.14210 478900.

 

 

*** you can find copies of both of these files at the following location:

/usr/local/gromacs/share/gromacs/top/

 

x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp

***Note: for some reason it does not generate SWNT_6_6_144.rtp

 

editconf -f SWNT_6_6_144.gro -o SWNT_6_6_144.gro  -d 0.5

 

genbox -cp SWNT_6_6_144.gro  -cs -o SWNT_6_6_144_b4em.gro -p
SWNT_6_6_144.top -maxsol 300

 

grompp -f em3.mdp -r SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top -o -maxwarn
310

 


***

 

 em3.mdp###  Can find a copy at: http://cs86.com/CNSE/em3.mdp

 

title= SWNT_6_6_144

cpp  = cpp

include  = /usr/local/gromacs/share/gromacs/top/

define   = -DFLEX_SPC

integrator   = md

dt   = 0.002

nsteps   = 50

nstxout  = 5000

nstvout  = 5000

nstlog   = 5000

nstenergy= 250

nstxtcout= 250

xtc_grps = Protein

energygrps   = Protein  SOL

nstlist  = 10

ns_type  = grid

rlist= 0.8

coulombtype  = cut-off

rcoulomb = 1.4

rvdw = 0.8

tcoupl   = Berendsen

tc-grps  = Protein  SOL

tau_t= 0.1  0.1

ref_t= 300  300

Pcoupl   = Berendsen

tau_p= 1.0

compressibility  = 4.5e-5

ref_p= 1.0

gen_vel  = yes

gen_temp = 300

gen_seed = 173529

constraints  = all-bonds

 

**

 

This is what I get after running grommp:

 

 

 

-bash-3.00$ grompp -f em3.mdp -r SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top
-o -maxwarn 310

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

.

.

.

 

  -[no]renum   boolyes  Renumber atomtypes and minimize number of

atomtypes

 

creating statusfile for 1 node...

' for variable integrator, using 'md'

Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'

' for variable ns-type, using 'Grid'

Next time use one of: 'Grid' 'Simple'

' for variable coulombtype, using 'Cut-off'

Next time use one of: 'Cut-off' 'Reaction-Field'
'Generalized-Reaction-Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift'
'User' 'Generalized-Born' 'Reaction-Field-nec' 'Encad-shift' 'PME-User'

' for variable tcoupl, using 'No'

Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'

' for variable Pcoupl, using 'No'

Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'

' for variable gen-vel, using 'no'

Next time use one of: 'no' 'yes'

' for variable constraints, using 'none'

Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'

 

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.15#

checking input for internal consistency...

...ling cpp

: command not found

cpp exit code: 32512

 SWNT_6_6_144.top > gromppOpff2m'cs/top -DFLEX_SPC

' command is defined in the .mdp file

processing topology...

processing coordinates...

---

Program grompp, VERSION 3.3.1

Source code file: futil.c, line: 340

 

File input/output error:

conf.gro

---

 

"This May Come As a Shock" (F. Black)

 

 


***

 

 

Any help or advice is greatly appreciated!

 

~Christopher Stiles 
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA
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Re: [gmx-users] Implicit solvent simulation

[TJ Piggot]

Hi,

Just to let people know in case they are unaware there is a paper where 
implicit solvent models have been implemented in GROMACS, the paper can be 
found using the following link:


http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15814616

Tom

--On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel 
<[EMAIL PROTECTED]> wrote:



SeungPyo Hong wrote:

Thank you for your kind reply, Stephane.
Anyhow it is a little disappointing that Generalized-Born is not
implemented in Gromacs.



I've put it on the development TODO list (feel free to volunteer)

http://wiki.gromacs.org/index.php/Implicit_Solvent

The reason it is not there is because none of the developers has
considered it worthwhile.

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.

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Re: [gmx-users] Implicit solvent simulation

[David van der Spoel]

SeungPyo Hong wrote:

Thank you for your kind reply, Stephane.
Anyhow it is a little disappointing that Generalized-Born is not 
implemented in Gromacs.




I've put it on the development TODO list (feel free to volunteer)

http://wiki.gromacs.org/index.php/Implicit_Solvent

The reason it is not there is because none of the developers has 
considered it worthwhile.


--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] Implicit solvent simulation

[SeungPyo Hong]

Thank you for your kind reply, Stephane.
Anyhow it is a little disappointing that Generalized-Born is not implemented
in Gromacs.

Sincerely,
Seungpyo Hong

On 7/16/07, Stéphane Téletchéa <[EMAIL PROTECTED]> wrote:


SeungPyo Hong a écrit :
> Dear gmx-users,
>
> Recently I want to perform MD for protein with implicit solvent model.
> Gromacs does not seem to support it.
> Could you let me know where to find information about implicit solvent
> simulation with Gromacs?
> Also I will be glad if you tell me your opinion about the implicit
> solvent simulation to protein.
>
> Thank you.
>

There is no Generalised-Born approach implemented (at least available)
but you may consider reaction field. See chapter 7, paragraph
"Electrostatics and VdW".

Cheers,
Stéphane

--
Stéphane Téletchéa, PhD.  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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Re: [gmx-users] Magic number error

[David van der Spoel]

Erik Lindahl wrote:

Hi,

Great that you solved it.

For the record, this is an excellent example why you should never, ever, 
use "soft" NFS mounts. If you stick to "hard" mounts the clients might 
hang while the server isn't responding, but at least you won't lose data.



of course you will have to reboot half your cluster, but hey... :)

Cheers,

Erik


On Jul 18, 2007, at 2:48 PM, zazeri wrote:


Thanks to Tsjerk Wassenaar, Yang Ye and Chris Neale.
My simulation is running very well! ;)
I put that to run on a computer with local HD.
Really, the problem was overload of NFS server.

Thanks again.


Fernando Lopes
Dept. of Physics
UNESP - São José do Rio Preto - SP - Brazil





--- Tsjerk Wassenaar <[EMAIL PROTECTED]> escreveu:


Hi Fernando,

Did you try using version 3.2 yourself?

Tsjerk

On 7/14/07, zazeri <[EMAIL PROTECTED]> wrote:

Hi to all! :D

I'm facing a problem with the xtc file. It has

been

getting me the following error:

Program trjconv, VERSION 3.3.1
Source code file: xtcio.c, line: 83

Fatal error:
Magic Number Error in XTC file (read 0, should be
1995).

In the mailing list I've found a person who said
installing the gromacs version 3.2 the problem was
solved. (I'm using 3.3 version)
Could somebody confirm it for me ?

Maybe could it be the case of correcting the code

in

xtcio.c ? And how should it be?

Thanks in advance!

Fernando Lopes
Dept. of Physics
UNESP - São José do Rio Preto - SP - Brazil










 


Novo Yahoo! Cadê? - Experimente uma nova busca.
http://yahoo.com.br/oqueeuganhocomisso
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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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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] Magic number error

[Erik Lindahl]

Hi,

Great that you solved it.

For the record, this is an excellent example why you should never,  
ever, use "soft" NFS mounts. If you stick to "hard" mounts the  
clients might hang while the server isn't responding, but at least  
you won't lose data.


Cheers,

Erik


On Jul 18, 2007, at 2:48 PM, zazeri wrote:


Thanks to Tsjerk Wassenaar, Yang Ye and Chris Neale.
My simulation is running very well! ;)
I put that to run on a computer with local HD.
Really, the problem was overload of NFS server.

Thanks again.


Fernando Lopes
Dept. of Physics
UNESP - São José do Rio Preto - SP - Brazil





--- Tsjerk Wassenaar <[EMAIL PROTECTED]> escreveu:


Hi Fernando,

Did you try using version 3.2 yourself?

Tsjerk

On 7/14/07, zazeri <[EMAIL PROTECTED]> wrote:

Hi to all! :D

I'm facing a problem with the xtc file. It has

been

getting me the following error:

Program trjconv, VERSION 3.3.1
Source code file: xtcio.c, line: 83

Fatal error:
Magic Number Error in XTC file (read 0, should be
1995).

In the mailing list I've found a person who said
installing the gromacs version 3.2 the problem was
solved. (I'm using 3.3 version)
Could somebody confirm it for me ?

Maybe could it be the case of correcting the code

in

xtcio.c ? And how should it be?

Thanks in advance!

Fernando Lopes
Dept. of Physics
UNESP - São José do Rio Preto - SP - Brazil










__ 
__

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http://yahoo.com.br/oqueeuganhocomisso
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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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Re: Re: [gmx-users] Magic number error

[zazeri]

Thanks to Tsjerk Wassenaar, Yang Ye and Chris Neale.
My simulation is running very well! ;)
I put that to run on a computer with local HD.
Really, the problem was overload of NFS server.

Thanks again.


Fernando Lopes
Dept. of Physics
UNESP - São José do Rio Preto - SP - Brazil





--- Tsjerk Wassenaar <[EMAIL PROTECTED]> escreveu:

> Hi Fernando,
> 
> Did you try using version 3.2 yourself?
> 
> Tsjerk
> 
> On 7/14/07, zazeri <[EMAIL PROTECTED]> wrote:
> > Hi to all! :D
> >
> > I'm facing a problem with the xtc file. It has
> been
> > getting me the following error:
> >
> > Program trjconv, VERSION 3.3.1
> > Source code file: xtcio.c, line: 83
> >
> > Fatal error:
> > Magic Number Error in XTC file (read 0, should be
> > 1995).
> >
> > In the mailing list I've found a person who said
> > installing the gromacs version 3.2 the problem was
> > solved. (I'm using 3.3 version)
> > Could somebody confirm it for me ?
> >
> > Maybe could it be the case of correcting the code
> in
> > xtcio.c ? And how should it be?
> >
> > Thanks in advance!
> >
> > Fernando Lopes
> > Dept. of Physics
> > UNESP - São José do Rio Preto - SP - Brazil
> >
> >
> >
> >
> >
> >
> >
> >
>

> > Novo Yahoo! Cadê? - Experimente uma nova busca.
> > http://yahoo.com.br/oqueeuganhocomisso
> > ___
> > 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
> >
> 
> 
> -- 
> 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
> ___
> 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
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> 



   

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Re: [gmx-users] Runtime need of cpp.exe

[Erik Lindahl]

Hi,


Can we use other (native windows) c preprocessor ?
As it says explicitly in the manual, you can use any preprocessor you  
want. The default force fields have #include and #define statements  
meant for a C preprocessor, but it's just a matter of pushing the  
input files through the specified preprocessor, whatever it might be.


However, last time I checked windows didn't ship with a default C  
preprocessor, so you'd have to install MSVC just for using grompp.  
It's also a proprietary product that you are not allowed to copy e.g.  
on cluster nodes, not to mention Microsoft would probably get upset  
if you made it available for download.


Cheers,

Erik

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Re: [gmx-users] Runtime need of cpp.exe

[Yang Ye]

If cpp is not runnable, I would wonder what those GCC guys are working 
and how you have compiled GROMACS?


On 7/18/2007 4:23 PM, Utkal Ranjan Pradhan wrote:

…. OK.
Again, the shipping Win32 version of cpp.exe is perfectly working with Gromacs 
64-bit on a opetron m/c which is a x86-64 box.
But I guess it (the above cpp.exe) may not work on pure x64 m/c as its not a 
valid x64 application.
Is there a x64 port of cpp.exe is available ?
Can we use other (native windows) c preprocessor ?
 
Sorry, if I’m making silly queries.
 
Thank you
 
 
 
Hi Utkal,
 
Cpp.exe is called by grompp to preprocess the topology.
 
Tsjerk
 
On 7/18/07, Utkal Ranjan Pradhan http://www.gromacs.org/mailman/listinfo/gmx-users>> wrote:

>/ /
>/ /
>/ /
>/ /
>/ Thank you for your reply./
>/ /
>/ /
>/ /
>/ But still confused WHY CPP.EXE IS REQUIRED AT RUNTIME ?/
>/ /
>/ (Note that, I can build gromacs without cpp.exe with MS VS 2005, but while/
>/ running applications like mdrun, it looks for cpp.exe L)/
>/ /
>/ /
>/ /
>/ /
>/ /
>/ Thank You;/
>/ /
>/ URPradhan At Gmail Dot Com/
>/ /
>/ /
>/ David van der Spoel wrote:/
>/ > Utkal Ranjan Pradhan wrote:/
>/ >> Friends/
>/ >>/
>/ >>/
>/ >>/
>/ >> As I know cpp.exe is a GNU port for C Preprocessor for Windows and/
>/ >> which is required to compile the Gromacs code./
>/ >>/
>/ >> But I'm confused, Why it is required during runtime of Gromacs/
>/ >> applications ?/
>/ >>/
>/ >> And I have the Win32 version of cpp.exe, will it work for x64 (=Win64) ?/
>/ >>/
>/ >> What is the Windows native equivalent of cpp.exe ? Is it cl.exe ?/
>/ >>/
>/ >> How can I remove the runtime dependency of cpp.exe for gromacs/
>/ >> applications ?/
>/ >/
>/ > by writing an implementation of the cpp and donating it to the gromacs/
>/ > project. In fact, it wouldn't be so hard, since we are only using a few/
>/ > features in practice:/
>/ > #include/
>/ > #ifdef #else #endif/
>/ > #define/
>/ >/
>/ > Please provide a simple C program that takes a file, searches for these/
>/ > commands and does the same what the cpp does./
>/ >/
>/ >/
>/ see also/
>/ http://wiki.gromacs.org/index.php/Cpp_replacement/
>/ /
>/ --/
>/ David van der Spoel, Ph.D./
>/ Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University./
>/ Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax:/
>/ +4618511755./
>/ spoel at xray.bmc.uu.sespoel at gromacs.org/
>/ http://folding.bmc.uu.se/
>/ /
>/ /
>/ /
>/ ___/
>/ gmx-users mailing listgmx-users at 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 gmx-users-request at gromacs.org. 
/
>/ Can't post? Read/
>/ http://www.gromacs.org/mailing_lists/users.php/
>/ /
 
 
--

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

Thank You;

URPradhan At Gmail Dot Com



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[gmx-users] Runtime need of cpp.exe

[Utkal Ranjan Pradhan]

.. OK.
Again, the shipping Win32 version of cpp.exe is perfectly working with
Gromacs 64-bit on a opetron m/c which is a x86-64 box.
But I guess it (the above cpp.exe) may not work on pure x64 m/c as its not a
valid x64 application.
Is there a x64 port of cpp.exe is available ?
Can we use other (native windows) c preprocessor ?
 
Sorry, if I'm making silly queries.
 
Thank you
 
 
 
Hi Utkal,
 
Cpp.exe is called by grompp to preprocess the topology.
 
Tsjerk
 
On 7/18/07, Utkal Ranjan Pradhan http://www.gromacs.org/mailman/listinfo/gmx-users> > wrote:
> 
> 
> 
> 
> Thank you for your reply.
> 
> 
> 
> But still confused WHY CPP.EXE IS REQUIRED AT RUNTIME ?
> 
> (Note that, I can build gromacs without cpp.exe with MS VS 2005, but while
> running applications like mdrun, it looks for cpp.exe L)
> 
> 
> 
> 
> 
> Thank You;
> 
> URPradhan At Gmail Dot Com
> 
> 
> David van der Spoel wrote:
> > Utkal Ranjan Pradhan wrote:
> >> Friends
> >>
> >>
> >>
> >> As I know cpp.exe is a GNU port for C Preprocessor for Windows and
> >> which is required to compile the Gromacs code.
> >>
> >> But I'm confused, Why it is required during runtime of Gromacs
> >> applications ?
> >>
> >> And I have the Win32 version of cpp.exe, will it work for x64 (=Win64)
?
> >>
> >> What is the Windows native equivalent of cpp.exe ? Is it cl.exe ?
> >>
> >> How can I remove the runtime dependency of cpp.exe for gromacs
> >> applications ?
> >
> > by writing an implementation of the cpp and donating it to the gromacs
> > project. In fact, it wouldn't be so hard, since we are only using a few
> > features in practice:
> > #include
> > #ifdef #else #endif
> > #define
> >
> > Please provide a simple C program that takes a file, searches for these
> > commands and does the same what the cpp does.
> >
> >
> see also
> http://wiki.gromacs.org/index.php/Cpp_replacement
> 
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax:
> +4618511755.
> spoel at xray.bmc.uu.sespoel at gromacs.org
> http://folding.bmc.uu.se
> 
> 
> 
> ___
> gmx-users mailing listgmx-users at 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 gmx-users-request at gromacs.org.
 
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 
 
 
-- 
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

 

 

 

Thank You;

URPradhan At Gmail Dot Com

 

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Re: [gmx-users] Runtime need of cpp.exe

[Tsjerk Wassenaar]

Hi Utkal,

Cpp.exe is called by grompp to preprocess the topology.

Tsjerk

On 7/18/07, Utkal Ranjan Pradhan <[EMAIL PROTECTED]> wrote:





Thank you for your reply.



But still confused WHY CPP.EXE IS REQUIRED AT RUNTIME ?

(Note that, I can build gromacs without cpp.exe with MS VS 2005, but while
running applications like mdrun, it looks for cpp.exe L)





Thank You;

URPradhan At Gmail Dot Com


David van der Spoel wrote:
> Utkal Ranjan Pradhan wrote:
>> Friends
>>
>>
>>
>> As I know cpp.exe is a GNU port for C Preprocessor for Windows and
>> which is required to compile the Gromacs code.
>>
>> But I'm confused, Why it is required during runtime of Gromacs
>> applications ?
>>
>> And I have the Win32 version of cpp.exe, will it work for x64 (=Win64) ?
>>
>> What is the Windows native equivalent of cpp.exe ? Is it cl.exe ?
>>
>> How can I remove the runtime dependency of cpp.exe for gromacs
>> applications ?
>
> by writing an implementation of the cpp and donating it to the gromacs
> project. In fact, it wouldn't be so hard, since we are only using a few
> features in practice:
> #include
> #ifdef #else #endif
> #define
>
> Please provide a simple C program that takes a file, searches for these
> commands and does the same what the cpp does.
>
>
see also
http://wiki.gromacs.org/index.php/Cpp_replacement

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax:
+4618511755.
spoel at xray.bmc.uu.sespoel at gromacs.org
http://folding.bmc.uu.se



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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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[gmx-users] Runtime need of cpp.exe

[Utkal Ranjan Pradhan]

Thank you for your reply.

 

But still confused WHY CPP.EXE IS REQUIRED AT RUNTIME ?

(Note that, I can build gromacs without cpp.exe with MS VS 2005, but while
running applications like mdrun, it looks for cpp.exe L)

 

 

Thank You;

URPradhan At Gmail Dot Com

 

 
David van der Spoel wrote:
> Utkal Ranjan Pradhan wrote:
>> Friends
>> 
>>  
>> 
>> As I know cpp.exe is a GNU port for C Preprocessor for Windows and 
>> which is required to compile the Gromacs code.
>> 
>> But I'm confused, Why it is required during runtime of Gromacs 
>> applications ?
>> 
>> And I have the Win32 version of cpp.exe, will it work for x64 (=Win64) ?
>> 
>> What is the Windows native equivalent of cpp.exe ? Is it cl.exe ?
>> 
>> How can I remove the runtime dependency of cpp.exe for gromacs 
>> applications ?
> 
> by writing an implementation of the cpp and donating it to the gromacs 
> project. In fact, it wouldn't be so hard, since we are only using a few 
> features in practice:
> #include
> #ifdef #else #endif
> #define
> 
> Please provide a simple C program that takes a file, searches for these 
> commands and does the same what the cpp does.
> 
> 
see also
http://wiki.gromacs.org/index.php/Cpp_replacement
 
-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax:
+4618511755.
spoel at xray.bmc.uu.se 
spoel at gromacs.org 
http://folding.bmc.uu.se

 

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Re: [gmx-users] Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run

[David van der Spoel]

Jim Kress wrote:
I ran a parallel (mpi) compiled version of gromacs using the following 
command line:


$ mpirun -np 5 mdrun_mpi -s topol.tpr -np 5 -v

At the end of the file md0.log I found:

M E G A - F L O P S   A C C O U N T I N G

Parallel run - timing based on wallclock.
   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
   T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
   NF=No Forces

 Computing:M-Number M-Flops  % of Flops
---
 Coulomb + LJ [W4-W4]876.631638   234060.64734688.0
 Outer nonbonded loop692.459088 6924.590880 2.6
 NS-Pairs457.344228 9604.228788 3.6
 Reset In Box 13.782888  124.045992 0.0
 Shift-X 137.773776  826.642656 0.3
 CG-CoM3.445722   99.925938 0.0
 Sum Forces  206.660664  206.660664 0.1
 Virial   70.237023 1264.266414 0.5
 Update   68.886888 2135.493528 0.8
 Stop-CM  68.88  688.80 0.3
 P-Coupling   68.886888  413.321328 0.2
 Calc-Ekin68.893776 1860.131952 0.7
 Constraint-V 68.886888  413.321328 0.2
 Constraint-Vir   51.675498 1240.211952 0.5
 Settle   17.225166 5563.728618 2.1
 Virtual Site 3   17.221722  637.203714 0.2
---
 Total266063.221098   100.0
---

   NODE (s)   Real (s)  (%)
   Time:   3344.000   3344.000100.0
   55:44
   (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:  0.262 79.564  0.517 46.444

Detailed load balancing info in percentage of average
TypeNODE:  0   1   2   3   4 Scaling
---
Coulomb + LJ [W4-W4]:118  94 101 104  80 84%
Outer nonbonded loop: 97  98  98 103 102 96%
   NS-Pairs:116  94 101 104  82 85%
   Reset In Box: 99 100  99 100  99 99%
Shift-X: 99 100  99 100  99 99%
 CG-CoM: 99 100  99 100  99 99%
 Sum Forces: 99 100  99  99  99 99%
 Virial: 99 100  99 100  99 99%
 Update: 99 100  99 100  99 99%
Stop-CM: 99 100  99 100  99 99%
 P-Coupling: 99 100  99 100  99 99%
  Calc-Ekin: 99 100  99 100  99 99%
   Constraint-V: 99 100  99 100  99 99%
 Constraint-Vir: 99 100  99 100  99 99%
 Settle: 99 100  99 100  99 99%
 Virtual Site 3: 99 100  99 100  99 99%

Total Force:118  94 101 104  81 84%


Total Shake: 99 100  99 100  99 99%


Total Scaling: 85% of max performance

Finished mdrun on node 0 Sat Jul 14 23:32:32 2007


Now, I tried the same calculation on one node and found the following at 
the end of the file md.log:


M E G A - F L O P S   A C C O U N T I N G

   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
   T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
   NF=No Forces

 Computing:M-Number M-Flops  % of Flops
---
 Coulomb + LJ [W4-W4]875.182588   233673.75099688.0
 Outer nonbonded loop688.853376 6888.533760 2.6
 NS-Pairs456.997574 9596.949054 3.6
 Reset In Box 13.782888  124.045992 0.0
 Shift-X 137.773776  826.642656 0.3
 CG-CoM3.445722   99.925938 0.0
 Virial   69.156915 1244.824470 0.5
 Update   68.886888 2135.493528 0.8
 Stop-CM  68.88  688.80 0.3
 P-Coupling   68.886888  413.321328 0.2
 Calc-Ekin68.893776 1860.131952 0.7
 Constraint-V 68.886888  413.321328 0.2
 Constraint-Vir   51.675498 1240.211952 0.5
 Settle   17.225166 5563.728618 2.1
 Virtual Site 3   17.221722  637.203714 0.2
---
 Total265406.885286   100.0
---

   NODE (s)   Real (s)  (%)
   Time:165.870167.000 99.3
   2:45
   (Mnbf/s)   (GFlops)   (ns/da

Re: [gmx-users] Runtime need of cpp.exe

[David van der Spoel]

David van der Spoel wrote:

Utkal Ranjan Pradhan wrote:

Friends

 

As I know cpp.exe is a GNU port for C Preprocessor for Windows and 
which is required to compile the Gromacs code.


But I’m confused, Why it is required during runtime of Gromacs 
applications ?


And I have the Win32 version of cpp.exe, will it work for x64 (=Win64) ?

What is the Windows native equivalent of cpp.exe ? Is it cl.exe ?

How can I remove the runtime dependency of cpp.exe for gromacs 
applications ?


by writing an implementation of the cpp and donating it to the gromacs 
project. In fact, it wouldn't be so hard, since we are only using a few 
features in practice:

#include
#ifdef #else #endif
#define

Please provide a simple C program that takes a file, searches for these 
commands and does the same what the cpp does.




see also
http://wiki.gromacs.org/index.php/Cpp_replacement

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] Runtime need of cpp.exe

[David van der Spoel]

Utkal Ranjan Pradhan wrote:

Friends

 

As I know cpp.exe is a GNU port for C Preprocessor for Windows and which 
is required to compile the Gromacs code.


But I’m confused, Why it is required during runtime of Gromacs 
applications ?


And I have the Win32 version of cpp.exe, will it work for x64 (=Win64) ?

What is the Windows native equivalent of cpp.exe ? Is it cl.exe ?

How can I remove the runtime dependency of cpp.exe for gromacs 
applications ?


by writing an implementation of the cpp and donating it to the gromacs 
project. In fact, it wouldn't be so hard, since we are only using a few 
features in practice:

#include
#ifdef #else #endif
#define

Please provide a simple C program that takes a file, searches for these 
commands and does the same what the cpp does.



--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
___
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