[gmx-users] Re: WCA and free energy calculations

[David Mobley]

Hi,

I'm CCing the users list on this since it might be of general interest.


 I
can't begin to tell you already how much help you've given me with your gromacs
user-list posts and free energy tutorial.


Glad I can help!


I was searching the Gromacs user list and came across a thread by you titled:
tabulated nonbonded interactions and free energy calculations.

I'm trying to do exactly the same thing that you described, using the WCA LJ
potential and free energy calculations.  No one ever responded to this thread,
but I was wondering if you figured out the answer?  Also, just to confirm that
I'm not spinning my wheels did you get the WCA LJ potential to work using the
user specified potential function?


So, no one ever responded to that thread, as you noticed. But my end
conclusion was that the tabulated nonbonded interactions know nothing
about lambda. So while one could implement the WCA separation using
tabulated nonbonded interactions, one couldn't use it to do free
energy calculations in a straightforward way, at least not
simultaneously with the soft core potentials I wanted to use (where
the effective radius is modified as a function of lambda). So I've put
it on the back burner for now. I guess you could in principle get WCA
to work with linear lambda scaing, but there is a lot of work in the
literature indicating that linear scaling is bad for transformations
involving insertion or deletion of LJ sites, which is presumably the
point of using the WCA separation in the first place.

Anyway -- I think that all means that one would actually need to
implement WCA into GROMACS to be able to use it for free energy
calculations.

I hope this makes sense. Please let me know if any of it needs further
explanation. Developers are welcome to weigh in if I'm going wrong
here anywhere...

Thanks,
David
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Re: [gmx-users] superimpose pdbs

[Yang Ye]

Pymol
http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/

It has a bit ease of use than g_confrm that it offers more richer 
choices for selecting atoms to be matched. See what fits to your needs.


Regards,
Yang Ye

On 6/25/2007 1:10 AM, Alan wrote:

Hi!

It may be a bit GMX off-topic: I am looking for a command line 
superimpose application that would be able to get all individual pdb 
files in folder and generated new pdb versions of them 3D superimposed.


Something like what SuperPose 
(http://wishart.biology.ualberta.ca/SuperPose/help.html) does, but 
then locally in my computer.


Many thanks in advance.

Cheers,
Alan

--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28 <<


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Re: [gmx-users] Energy minimization problem with Double precision and mpi

[David van der Spoel]

Josiah Zayner wrote:



-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of David van der Spoel
Sent: Sunday, June 24, 2007 4:18 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy minimization problem with Double precision
andmpi

Josiah Zayner wrote:

-Original Message-
From: [EMAIL PROTECTED] [mailto:gmx-users-

[EMAIL PROTECTED]

On Behalf Of David van der Spoel
Sent: Saturday, June 23, 2007 4:36 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy minimization problem with Double

precision

andmpi

Josiah Zayner wrote:

I managed to install mdrun_d from CVS and the problem is fixed



you didn't say which cvs solved your problem. was it the
release_3_3_patches branch?

Mdrun_d says version: 3.3.99_development_20070413
It was the main branch.


OK,

this branch is not yet quite stable, we are still testing things there.
It would be good to know whether the  release_3_3_patches branch also
solves your problem.


Installing the release-3-3-patches branch also solves the problem. I only
tested it on two nodes ie. -np 2 but I assume it would also work for more.


Thanks, that is good to hear. It could be due to parallel minimization, 
but if it is fixed in CVS I won't investigate it further.


--
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] Energy minimization problem with Double precision and mpi

[Josiah Zayner]

> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> On Behalf Of David van der Spoel
> Sent: Sunday, June 24, 2007 4:18 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Energy minimization problem with Double precision
> andmpi
> 
> Josiah Zayner wrote:
> > -Original Message-
> > From: [EMAIL PROTECTED] [mailto:gmx-users-
> [EMAIL PROTECTED]
> > On Behalf Of David van der Spoel
> > Sent: Saturday, June 23, 2007 4:36 PM
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] Energy minimization problem with Double
> precision
> > andmpi
> >
> > Josiah Zayner wrote:
> >> I managed to install mdrun_d from CVS and the problem is fixed
> >
> >
> >>> you didn't say which cvs solved your problem. was it the
> >>> release_3_3_patches branch?
> >
> > Mdrun_d says version: 3.3.99_development_20070413
> > It was the main branch.
> >
> OK,
> 
> this branch is not yet quite stable, we are still testing things there.
> It would be good to know whether the  release_3_3_patches branch also
> solves your problem.

Installing the release-3-3-patches branch also solves the problem. I only
tested it on two nodes ie. -np 2 but I assume it would also work for more.

> 
> --
> 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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RES: [gmx-users] superimpose pdbs

[Caio Julio Martins Veloso]

Hi Alan,

You may use TOPOFIT. 

Caio.
  -Mensagem original-
  De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] nome de Alan
  Enviada em: domingo, 24 de junho de 2007 14:11
  Para: Gromacs
  Assunto: [gmx-users] superimpose pdbs


  Hi!


  It may be a bit GMX off-topic: I am looking for a command line superimpose 
application that would be able to get all individual pdb files in folder and 
generated new pdb versions of them 3D superimposed. 


  Something like what SuperPose 
(http://wishart.biology.ualberta.ca/SuperPose/help.html) does, but then locally 
in my computer. 


  Many thanks in advance.


  Cheers,
  Alan

  -- 
  Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate 
  Department of Biochemistry, University of Cambridge.
  80 Tennis Court Road, Cambridge CB2 1GA, UK.
  >>http://www.bio.cam.ac.uk/~awd28<< ___
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[gmx-users] Regarding minimization of POPE:POPG lipid bilayer

[chris . neale]

  I built a POPE:POPG bilayer in 3:1 ratio.


Simplify. Start with pure POPE and pure POPG first.


When I am minimizing the  bilayer, bonds in head groups are breaking
in POPE and POPG lipid  molecules.


Your topologies are incorrect. Start with a simple test system: a
single POPE in vaccuum.

while creating *.tpr file using the above file for minimization, I  
am getting fallowing message.


  calling /lib/cpp...
  In file included from pg-pe.top:5:
  dpopg.itp:10:8: warning: multi-line string literals are deprecated


Why not take a look at line 10 (or line 8) in dpopg.itp?


You are still a long way from simulating a protein in the bilayer. May
I recommend that you try a little harder to solve your problems before
posting (e.g. by reading the warning messages carefully and seeing
what they mean for yourself, or by trying to find a simpler test
system to narrow down the problem). In this way you will avoid  
decreasing your likelihood of receiving answers to the harder problems  
you may encounter.



Good luck.

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Re: [gmx-users] superimpose pdbs

[David van der Spoel]

Alan wrote:

Hi!

It may be a bit GMX off-topic: I am looking for a command line 
superimpose application that would be able to get all individual pdb 
files in folder and generated new pdb versions of them 3D superimposed.



g_confrms

Something like what SuperPose 
(http://wishart.biology.ualberta.ca/SuperPose/help.html) does, but then 
locally in my computer.


Many thanks in advance.

Cheers,
Alan

--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
 >>http://www.bio.cam.ac.uk/~awd28<<




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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] superimpose pdbs

[Alan]

Hi!
It may be a bit GMX off-topic: I am looking for a command line superimpose
application that would be able to get all individual pdb files in folder and
generated new pdb versions of them 3D superimposed.

Something like what SuperPose (
http://wishart.biology.ualberta.ca/SuperPose/help.html) does, but then
locally in my computer.

Many thanks in advance.

Cheers,
Alan

--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

http://www.bio.cam.ac.uk/~awd28<<
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Re: [gmx-users] Energy minimization problem with Double precision and mpi

[David van der Spoel]

Josiah Zayner wrote:

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of David van der Spoel
Sent: Saturday, June 23, 2007 4:36 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy minimization problem with Double precision
andmpi

Josiah Zayner wrote:

I managed to install mdrun_d from CVS and the problem is fixed



you didn't say which cvs solved your problem. was it the 
release_3_3_patches branch?


Mdrun_d says version: 3.3.99_development_20070413
It was the main branch.


OK,

this branch is not yet quite stable, we are still testing things there. 
It would be good to know whether the  release_3_3_patches branch also 
solves your problem.


--
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] editconf -translate help

[David van der Spoel]

Shayla Fitzsimmons wrote:

I have a box which contains a slab of carbon (solid) that is centered within the
box.  However, I want the slab to be at the very right side of the box - I know
I must use editconf -translate to do this, however I cannot seem to make it
work.

The slab is centered has the same height and width (y and z coordinates) of the
box, however it is one third of the length (the x coordinate).  Graphically, at
the moment, it looks like this:
 _
|   xxx   |
|   xxx   |
|___xxx___|

Where 'xx' is my slab (that is how the view comes up when I open the file in
rasmol).

The dimensions of the box (as listed in the .gro file) are 13.90030 4.02160
5.36640

As I previously said, I want the slab to be on the right side of the box, not
the center, however I have tried several different things and it does not seem
to want to work for me (however, I am unsure if I am using the proper values
for -translate).

What X Y Z coordinates should I use for this to translate it?



the difference between new and old com. most likely 5 0 0 will do the trick.


Thanks!
S F
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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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