[gmx-users] [Fwd: Oueries]

[David van der Spoel]

 Original Message 
Subject:Oueries
Date:   Mon, 10 Sep 2007 08:08:40 +0100 (BST)
From:   Moutusi Manna <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]



Hi,
I have started using GROMACS recently. As per information GROMACS is
the fasted MD pacage . But, when I perform "mdrun" it takes only "1-10%"
of CPU % & as a result job becomes very slow .
Please suggest how I can increase the speed of simulation .
 Thanks,

   Moutusi


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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] [Fwd: Oueries]

[Yang Ye]

Try running mdrun with -nice 0.
 
Regards,
Yang Ye



- Original Message 
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
Sent: Monday, September 10, 2007 3:31:35 PM
Subject: [gmx-users] [Fwd: Oueries]


 Original Message 
Subject: Oueries
Date: Mon, 10 Sep 2007 08:08:40 +0100 (BST)
From: Moutusi Manna <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]



Hi,
 I have started using GROMACS recently. As per information GROMACS is
the fasted MD pacage . But, when I perform "mdrun" it takes only "1-10%"
of CPU % & as a result job becomes very slow .
 Please suggest how I can increase the speed of simulation .
  Thanks,

Moutusi


Get the freedom to save as many mails as you wish. Click here to know
how.

 



-- 
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] [Fwd: Oueries]

[Mark Abraham]

David van der Spoel wrote:



 Original Message 
Subject: Oueries
Date: Mon, 10 Sep 2007 08:08:40 +0100 (BST)
From: Moutusi Manna <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]



Hi,
I have started using GROMACS recently. As per information GROMACS is
the fasted MD pacage . But, when I perform "mdrun" it takes only "1-10%"
of CPU % & as a result job becomes very slow .
Please suggest how I can increase the speed of simulation .
 Thanks,

   Moutusi


Hi,

I've started driving a Ferrari recently. I've heard they make the 
fastest cars. But, when I'm driving, I can't get above 100rpm and as a 
result kids on bikes go faster than me. Please suggest how I can 
increase the speed of driving.


Thanks,

Mark

P.S. Imagine how a Formula 1 driver would respond to my email, and 
you've got an idea how we're likely to respond to yours. :-)
P.P.S. People are generally happy to help, but you have to give them 
some information to work with.

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Re: [gmx-users] [Fwd: Oueries]

[sebastien santini]

maybe you could set the nicelevel to a higher priority 


David van der Spoel a écrit :



 Original Message 
Subject: Oueries
Date: Mon, 10 Sep 2007 08:08:40 +0100 (BST)
From: Moutusi Manna <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]



Hi,
I have started using GROMACS recently. As per information GROMACS is
the fasted MD pacage . But, when I perform "mdrun" it takes only "1-10%"
of CPU % & as a result job becomes very slow .
Please suggest how I can increase the speed of simulation .
 Thanks,

   Moutusi


Get the freedom to save as many mails as you wish. Click here to know
how.
 







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___

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http://sebastien.santini.free.fr

CBMN, Faculté Universitaire des Sciences Agronomiques  
Passage des déportés, 2  
B-5030 Gembloux, BELGIQUE


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Re: [gmx-users] Partial Charge Units in GROMACS.

[Yang Ye]

yes.

On 9/10/2007 9:34 AM, Travis Trudeau wrote:
My apologies if this question is rather elementary, but we are 
uncertain what the units of partial charge are in GROMACS (i.e. in 
library files like ffG43a1.rtp) - we are assuming they are units of 
elementary charge ( i.e. charge of one electron/proton = 1)
 
Thank-you.
 
-Travis Trudeau



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Re: [gmx-users] make_edi command options

[Tsjerk Wassenaar]

Anirban,

Exactly what it says in the manual: the indices of eigenvectors to
include; a string consisting of one or more numeric characters if
needed separated by spaces...

Tsjerk

On 9/10/07, Anirban Ghosh <[EMAIL PROTECTED]> wrote:
> Hi All,
> I want to use the make_edi command in GROMACS for creating the .edi file for
> analysing some eigenvectors. For using the make_edi command there is an
> option of selecting the algorithm (-linfix / -linacc / rdfix) with "string"
> value. I shall be glad if someone can tell me what value has to be given
> after -linfix as the string. What does this string specify? All suggestions
> are welcome.
>
> Regards,
>
>
>
> Anirban Ghosh
> M.Tech Bioinformatics
> University of Hyderabad
> Hyderabad - 500 046
> Andhra Pradesh
> India
>
>  
>  Why delete messages? Unlimited storage is just a click away.
>
>
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Utrecht University
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The Netherlands
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[gmx-users] make_edi command options

[Anirban Ghosh]

Hi All,
I want to use the make_edi command in GROMACS for creating the .edi file for 
analysing some eigenvectors. For using the make_edi command there is an option 
of selecting the algorithm (-linfix / -linacc / rdfix) with "string" value. I 
shall be glad if someone can tell me what value has to be given after -linfix 
as the string. What does this string specify? All suggestions are welcome.

Regards,


 
  Anirban Ghosh
  M.Tech Bioinformatics
  University of Hyderabad
  Hyderabad - 500 046
  Andhra Pradesh
  India

   
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[gmx-users] Generating a solvent box

[Dilraj Lama]

Hello gmx users,
I have a query to ask.It would be nice if someone could
suggest me on this.I have a tfe molecule generated using
InsightII program package.Now I would like to create a box
containing a fixed number of tfe molecules based on its
density.I tried using "genbox" and "genconf" for the
purpose but am not able to achieve my aim.If someone has
tried to do this before and have some idea, I would be
thankfull if you could shed some light on the subject.

Thanking you.
-- 
Dilraj Lama,
Graduate student,
Bioinformatics and Biomolecular Simualtion lab,
Dept. of BSBE;IITK-kanpur,
Uttar pradesh,India-208016.
email:[EMAIL PROTECTED],[EMAIL PROTECTED]
mob:09415473973

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Re: [gmx-users] Generating a solvent box

[Justin A. Lemkul]

Quoting Dilraj Lama <[EMAIL PROTECTED]>:

> Hello gmx users,
> I have a query to ask.It would be nice if someone could
> suggest me on this.I have a tfe molecule generated using
> InsightII program package.Now I would like to create a box
> containing a fixed number of tfe molecules based on its
> density.I tried using "genbox" and "genconf" for the
> purpose but am not able to achieve my aim.If someone has

What did you try (i.e., what commands did you issue)?  You should be able to
generate at least a regular arrangement of TFE molecules with genconf.

> tried to do this before and have some idea, I would be
> thankfull if you could shed some light on the subject.
>
> Thanking you.
> --
> Dilraj Lama,
> Graduate student,
> Bioinformatics and Biomolecular Simualtion lab,
> Dept. of BSBE;IITK-kanpur,
> Uttar pradesh,India-208016.
> email:[EMAIL PROTECTED],[EMAIL PROTECTED]
> mob:09415473973
>
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-Justin

==

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

==
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Re: [gmx-users] Generating a solvent box

[Dilraj Lama]

Hello justin,
 Here is what I did.I initially defined a cubic box into which
I placed the TFE molecule.This I did using editconf.Then I
used genconf with the follwing command.

 genconf_mpi -f tfe-box-four.gro -o out-four.pdb -nbox 5 5 5

Yes I am able to generate a regular arrangment of the TFE molecules.

But what I want to do now is to have a predfined cubic box dimension which
I want to solvate with a fixed number of TFE molecules corresponding to a
given density.

Thanks for your response.
> Quoting Dilraj Lama <[EMAIL PROTECTED]>:
>
>> Hello gmx users,
>> I have a query to ask.It would be nice if someone could
>> suggest me on this.I have a tfe molecule generated using
>> InsightII program package.Now I would like to create a box
>> containing a fixed number of tfe molecules based on its
>> density.I tried using "genbox" and "genconf" for the
>> purpose but am not able to achieve my aim.If someone has
>
> What did you try (i.e., what commands did you issue)?  You should be able
> to
> generate at least a regular arrangement of TFE molecules with genconf.
>
>> tried to do this before and have some idea, I would be
>> thankfull if you could shed some light on the subject.
>>
>> Thanking you.
>> --
>> Dilraj Lama,
>> Graduate student,
>> Bioinformatics and Biomolecular Simualtion lab,
>> Dept. of BSBE;IITK-kanpur,
>> Uttar pradesh,India-208016.
>> email:[EMAIL PROTECTED],[EMAIL PROTECTED]
>> mob:09415473973
>>
>> ___
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>>
>
> -Justin
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> [EMAIL PROTECTED] | (540) 231-9080
> http://bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
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>


-- 
Dilraj Lama,
Graduate student,
Bioinformatics and Biomolecular Simualtion lab,
Dept. of BSBE;IITK-kanpur,
Uttar pradesh,India-208016.
email:[EMAIL PROTECTED],[EMAIL PROTECTED]
mob:09415473973

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Re: [gmx-users] Generating a solvent box

[David van der Spoel]

Dilraj Lama wrote:

Hello justin,
 Here is what I did.I initially defined a cubic box into which
I placed the TFE molecule.This I did using editconf.Then I
used genconf with the follwing command.

 genconf_mpi -f tfe-box-four.gro -o out-four.pdb -nbox 5 5 5

Yes I am able to generate a regular arrangment of the TFE molecules.

But what I want to do now is to have a predfined cubic box dimension which
I want to solvate with a fixed number of TFE molecules corresponding to a
given density.


just do md with pressure coupling.


Thanks for your response.

Quoting Dilraj Lama <[EMAIL PROTECTED]>:


Hello gmx users,
I have a query to ask.It would be nice if someone could
suggest me on this.I have a tfe molecule generated using
InsightII program package.Now I would like to create a box
containing a fixed number of tfe molecules based on its
density.I tried using "genbox" and "genconf" for the
purpose but am not able to achieve my aim.If someone has

What did you try (i.e., what commands did you issue)?  You should be able
to
generate at least a regular arrangement of TFE molecules with genconf.


tried to do this before and have some idea, I would be
thankfull if you could shed some light on the subject.

Thanking you.
--
Dilraj Lama,
Graduate student,
Bioinformatics and Biomolecular Simualtion lab,
Dept. of BSBE;IITK-kanpur,
Uttar pradesh,India-208016.
email:[EMAIL PROTECTED],[EMAIL PROTECTED]
mob:09415473973

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-Justin

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

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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] Adding two peptides in a water box

[Triguero, Luciano O]

Hi Guys,
 
Thank very much for your time trying to help me with this issue. 
 
It seems from all your answers that adding two identical peptides, separated by 
a certain distance from each other, and then put them into a water box with 
ions is a simple task. However, it is still puzzling me. Although, I have 
analized very carefelly all your suggestions and proved them, my problem still 
remain unsolved. 
 
My last .gro file, the one containing the two petides with water and ions, 
lacks the H in the N-term of the first protein, and the O in the C-term of the 
second protein. 
 
John,
 
You suggested to me to use the -label option, but forgot to tell me from which 
gromacs program tool. The pdb2gmx version I have (VERSION 3.3.1) does not 
contain such a label. This option (-label) exists in the editconf, but it did 
not solve the problem.  Could you be more specific and tell me, how to use this 
option -label and to which tools it is connected? Please, I will appreciate any 
simple example.
 
Lars and Mark,
 
I always read your emails, they have helped me a lot in many different 
occacions, but this time I could not figure out 
any simple solution from your recommendations. I've read the manual, 
particularly chapter 5, but still there are things that I can not put together; 
perhaps that is why I can not solve this "rather" simple problem.
 
Let me explain once again, what I am trying to do. Perhaps, I was not clear 
enough the first time I put my problem in the list:
 
I want to simulate the interaction between two identical proteins solvateed in 
water. I think, I am familiar with GROMACS, and I know how to prepare, run and 
analyze a single solvate peptide.
 
Thus, following the same procedures, I started preparing my simulation with the 
two identical proteins.
 
I start from the PDB file of protein_A.pdb. Creates the protein_A.gro and 
protein_A.top file.
I applied translation and rotations to the protein_A.gro file (edifconf) and 
creates a new protein_B.gro file that I named protein_B.gro
I assume that the protein_A.top file is the same for protein_B.gro, so I don't 
need to run pdb2gmx again.
 
Thus, at this point I have two .gro files and one topology file. So, how do I 
modified the .gro files and the .top file 
to clearly indicate that I have two chains in my composed system?
 
P.S. I also read the pdb2gmx -h very carefully and did not find any second 
alternative. The -[no]merge flag, that might indicates to be useful for this 
type of problem, did not work either.
 
Please, I need your HELP!
 
All the best,
 
Luciano
 
 
 
 
 
 
 
Dr. Luciano Triguero College of Art and Science Department of Physics and 
Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 
Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938



From: [EMAIL PROTECTED] on behalf of Sheyore Omovie
Sent: Sat 9/8/2007 12:36 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Adding two peptides in a water box



Hi Luciano,
use the -label option to separately label the gro files (e.g A for the first 
peptide and B for the 2nd), before you cat them with an editor. pdb2gmx should 
now recognise them as separate molecules.
Rgds
John

> Date: Sat, 8 Sep 2007 15:43:33 +0200
> Subject: Re: [gmx-users] Adding two peptides in a water box
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> 
> > Hi Everybory,
> >
> > I would like to simulate the interaction between two separated peptides in
> > a water box. Every peptide needs to be N-and C-terminated. I have tried
> > different alternatives in order to create the corresponding GROMACS files
> > to start my simulation. I have used the GROMACS porograms tools as
> > described in the manual. However, I still have some problems and need of
> > your expeirences.
> >
> > This is what I do:
> >
> > 1.- I start from a pdb of one peptide.
> > 2.- Create the gro and top files. In this step I terminate the peptide
> > without any problem.
> > 3.- Apply corresponding translations and rotation to the existing gro file
> > (obtained in step 1) and create a new .gro file. This one is termed the
> > second peptide.
> > 4.- Cat them with an editor and save the result in a file named dimer.gro.
> > I can visualize it without any problem. So far, everything is going good.
> > 5.- HERE STARTS THE PROBLEM. I use dimer.gro as input to pdb2gmx to create
> > the new, dimer.top file. The pdb2gmx removes the hydrogens of the N-term
> > of one petide and the oxigen of the C-term in the second peptide.
> > Although, they are far apart.
> >
> > Does anyone know how to overcome this porblem?
> 
> Hi,
> why do you run pdb2gmx for the dimer? run it for the monomer, and then
> just put a "Protein 2" instead of a "Protein 1" (or however you name it)
> at the end of your topol.top file (just as is done for the water
> molecules, ions, etc).
> Lars
> >
> 
> > Thank in advance for you time.
> >
> > Ciao,
> >
> > Luciano
> >
> > Dr. 

[gmx-users] "check14" and "shuffle" options in grompp command

[WU Yanbin]

Hey, Everyone,
  Question about options for grompp command:
  (1) "check14": the description is "Remove 1-4 interactions without Van der
Waals". What's the meaning by "Van der Waals"? Does it mean if there is no
corresponding Van der Waals parameter defined in [ pairtypes ], the item in
[ pairs ] would be removed?
  (2) "shuffle": Is it compulsory for parallel running? I read from the
manual that it's a must.
  Thanks in advance.
   Yours Sincerely,
 WU Yanbin
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Re: [gmx-users] frozen group, pull code and COM motion removal

[Allen Smith]

In message <[EMAIL PROTECTED]> (on 9 September 2007 19:35:32
+0200), [EMAIL PROTECTED] (David van der Spoel) wrote:
>[someone] wrote:
>> Hi all,
>> 
>> Recently, I performed a simulation which have three groups: frozen group 
>> (there's no connections with the other groups), free group (peptide), 
>> mobile group (using AFM pulling of the pull code) . How should I set the 
>> comm._mode and comm _grps in the mdp file?
>> 
>more info please.

I believe at least part of the question is whether a frozen group will be
moved at all by the COM motion removal (e.g., if rotation of the rest of the
system to cancel out center-of-mass motion might do something like leaving
the frozen part behind).

  -Allen

-- 
Allen Smith  http://cesario.rutgers.edu/easmith/
There is only one sound argument for democracy, and that is the argument
that it is a crime for any man to hold himself out as better than other men,
and, above all, a most heinous offense for him to prove it. - H. L. Mencken
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Re: [gmx-users] "check14" and "shuffle" options in grompp command

[Yang Ye]

On 9/11/2007 7:05 AM, WU Yanbin wrote:

Hey, Everyone,
  Question about options for grompp command:
  (1) "check14": the description is "Remove 1-4 interactions without 
Van der Waals". What's the meaning by "Van der Waals"? Does it mean if 
there is no corresponding Van der Waals parameter defined in [ 
pairtypes ], the item in [ pairs ] would be removed?

Yes. From your later sentence, I think that you got what VDW means.
  (2) "shuffle": Is it compulsory for parallel running? I read from 
the manual that it's a must.

No, although it helps it. It needs to be used together with sort.

  Thanks in advance.
   Yours Sincerely,
 WU Yanbin


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[gmx-users] Change in distances between two atom during MD

[Rui Li]

Hi all,

I want to get the plot of Change in distances between two atom during MD
simulation.
what program can I use?
Thank you in advance


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Re: [gmx-users] Change in distances between two atom during MD

[Mark Abraham]

Rui Li wrote:

Hi all,

I want to get the plot of Change in distances between two atom during MD
simulation.
what program can I use?


Manual section 7.4

Mark
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Re: [gmx-users] "check14" and "shuffle" options in grompp command

[David van der Spoel]

Yang Ye wrote:

On 9/11/2007 7:05 AM, WU Yanbin wrote:

Hey, Everyone,
  Question about options for grompp command:
  (1) "check14": the description is "Remove 1-4 interactions without 
Van der Waals". What's the meaning by "Van der Waals"? Does it mean if 
there is no corresponding Van der Waals parameter defined in [ 
pairtypes ], the item in [ pairs ] would be removed?

Yes. From your later sentence, I think that you got what VDW means.


So when the pair parameters are zero the interactions are not 
calculated, according to the GROMACS philosophy that we don't compute 
anything if we know the result is zero in advance.


  (2) "shuffle": Is it compulsory for parallel running? I read from 
the manual that it's a must.

No, although it helps it. It needs to be used together with sort.
Shuffle helps especially for mixed systems like membranes. Sort should 
be used with caution since it is difficult to unsort (whereas unshuffle 
is possible). These options will both disappear in gromacs 4.0




  Thanks in advance.
   Yours Sincerely,
 WU Yanbin


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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] Exclusions for aromatic residues

[한상화]

Hi,

In .rtp file of a GROMOS 96 force field (ffG43a1.rtp for example),
exclusions seem to be listed only for aromatic residues such as TYR, HIS,
and TRP.

Why is that so?

 

Sanghwa Han

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Re: [gmx-users] Exclusions for aromatic residues

[David van der Spoel]

한상화 wrote:

Hi,

In .rtp file of a GROMOS 96 force field (ffG43a1.rtp for example), 
exclusions seem to be listed only for aromatic residues such as TYR, 
HIS, and TRP.


Why is that so?

normally they are generated (chapter 4) but one can define extra 
exclusions. interactions within rings usualy just work to deform the 
rings which is undesired therefore they are turned off.
 


Sanghwa Han




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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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