Re: [gmx-users] sequence of mdrun commands

[Yongchul Chung]

Thanks Justin, and Tsjerk for the helpful comments. I think I can get away
with a simple for-loop as Justin recommended.

Greg


On Thu, Aug 25, 2011 at 4:14 PM, Tsjerk Wassenaar  wrote:

> Hey :
>
> In scripts, like on the command line, processes wait for earlier
> processes to finish, unless these are brought to the background using
> the ampersand '&' at the end of the line. If you want to execute
> something in the background in your script, to allow checking the
> progress automatically, for instance, you can make sure some later
> process does not start before the ones in the background finished by
> using the command 'wait':
>
> mdrun -deffnm [...] &
> wait
> grompp [...]
> mdrun -deffnm [...] &
> wait
> echo FINISHED
>
> Hope it helps,
>
> Tsjerk
>
> On Thu, Aug 25, 2011 at 9:14 PM, Justin A. Lemkul  wrote:
> >
> >
> > Yongchul Chung wrote:
> >>
> >> Hello gmx-users,
> >>
> >> I am trying to run a sequence of energy minimizations for a model
> polymer
> >> system. Currently, I do following steps manually:
> >> step 1) I run an energy minimization for a configuration. (using mdrun
> >> option)
> >> step 2) From the output of this configuration, I change something in the
> >> coordinate file then run the energy minimization. (using editconf
> option)
> >>
> >> I want to automate this process since the delay between runs is ~15
> >> minutes. My idea is that I can probably introduce time delay in scripts,
> but
> >> it would be nice if there's an option in GROMACS which allows for a
> sequence
> >> of mdruns. Does anyone aware of such option for GROMACS?
> >
> > No, this just sounds like a job for a simple for-loop.  No time delay
> > necessary, just set a counter for the number of iterations and run the
> > sequence of commands within the loop.
> >
> > -Justin
> >
> > --
> > 
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> interface
> > or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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Re: [gmx-users] sequence of mdrun commands

[Tsjerk Wassenaar]

Hey :

In scripts, like on the command line, processes wait for earlier
processes to finish, unless these are brought to the background using
the ampersand '&' at the end of the line. If you want to execute
something in the background in your script, to allow checking the
progress automatically, for instance, you can make sure some later
process does not start before the ones in the background finished by
using the command 'wait':

mdrun -deffnm [...] &
wait
grompp [...]
mdrun -deffnm [...] &
wait
echo FINISHED

Hope it helps,

Tsjerk

On Thu, Aug 25, 2011 at 9:14 PM, Justin A. Lemkul  wrote:
>
>
> Yongchul Chung wrote:
>>
>> Hello gmx-users,
>>
>> I am trying to run a sequence of energy minimizations for a model polymer
>> system. Currently, I do following steps manually:
>> step 1) I run an energy minimization for a configuration. (using mdrun
>> option)
>> step 2) From the output of this configuration, I change something in the
>> coordinate file then run the energy minimization. (using editconf option)
>>
>> I want to automate this process since the delay between runs is ~15
>> minutes. My idea is that I can probably introduce time delay in scripts, but
>> it would be nice if there's an option in GROMACS which allows for a sequence
>> of mdruns. Does anyone aware of such option for GROMACS?
>
> No, this just sounds like a job for a simple for-loop.  No time delay
> necessary, just set a counter for the number of iterations and run the
> sequence of commands within the loop.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] sequence of mdrun commands

[Justin A. Lemkul]

Yongchul Chung wrote:

Hello gmx-users,

I am trying to run a sequence of energy minimizations for a model 
polymer system. Currently, I do following steps manually:
step 1) I run an energy minimization for a configuration. (using mdrun 
option)
step 2) From the output of this configuration, I change something in the 
coordinate file then run the energy minimization. (using editconf option)


I want to automate this process since the delay between runs is ~15 
minutes. My idea is that I can probably introduce time delay in scripts, 
but it would be nice if there's an option in GROMACS which allows for a 
sequence of mdruns. Does anyone aware of such option for GROMACS? 



No, this just sounds like a job for a simple for-loop.  No time delay necessary, 
just set a counter for the number of iterations and run the sequence of commands 
within the loop.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] sequence of mdrun commands

[Yongchul Chung]

Hello gmx-users,

I am trying to run a sequence of energy minimizations for a model polymer
system. Currently, I do following steps manually:
step 1) I run an energy minimization for a configuration. (using mdrun
option)
step 2) From the output of this configuration, I change something in the
coordinate file then run the energy minimization. (using editconf option)

I want to automate this process since the delay between runs is ~15 minutes.
My idea is that I can probably introduce time delay in scripts, but it would
be nice if there's an option in GROMACS which allows for a sequence of
mdruns. Does anyone aware of such option for GROMACS?

Greg
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Re: [gmx-users] Obtaining protein structure

[Justin A. Lemkul]

Steven Neumann wrote:
Thank you for your help. I want to calculate binging free energy of 
small molecules to protein termini.
 


If you need high-quality structural data for disordered termini, you're unlikely 
to get a good model without a huge amount of modeling, refinement, and 
validation.  As Mark said, there's good reason why structural information for 
termini is hard to come by.  You've posed a rather ill-defined task, so you'd do 
well to invest some time in the literature for established procedures and means 
of validation for your results.


-Justin


Steven

On Thu, Aug 25, 2011 at 4:22 PM, Mark Abraham > wrote:


On 26/08/2011 1:16 AM, Steven Neumann wrote:

Dear Gromacs Users,
 
I want to do some simulations of the protein (its N anc C

terminals) which crystal structure does not exist.


There will normally be reasons why the termini do not have a defined
structure - often that this are in fact disordered. That will make
your life doing simulations considerably more difficult, and not
just in choosing a starting structure.



I submitted the sequence to www.proteinmodelportal.org
 obtaining different
structures based on different proteins from Protein Data Bank. For
instance my N terminal has 180 aa. Obtained models covers %Seq id
of 78% for 36 residues, 68% for 36 different residues, 62% of 36
another residues and many other models below 50%. The website
provides you with the PDB files of your query so sounds perfect as
you do not have to mutate every residue one by one.
The question is whether this is efficent and provide a good result
to use such protein in my simualtions? Is this app. too big? 


Depends what simulations you plan - but very likely you will not be
able to study more than one or two candidate structures.



What are the other ways to overcome this problem (obtain structure
of the protein which crystal structure does not exist?


Protein structure prediction is a field all of its own for a reason.
It's hard.

Mark

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: Convert drug Charmm topology to Gromacs

[Justin A. Lemkul]

Alexandre Suman de Araujo wrote:

Hi Fabian

As far as I know, the way to send your contribution is contacting 
someone who administrate the website. I think Justin is one of them.




Nope, I'm not an admin, but I can offer some help :)

You have to create an account on gromacs.org and then contact Rossen to be 
listed as a contributor.  You can then upload files.  This information is on the 
Gromacs homepage, along with a link to Rossen's email.  Then just go to the User 
Contributions section and add the file(s) (preferably a .tgz archive) along with 
a description.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: Convert drug Charmm topology to Gromacs

[Alexandre Suman de Araujo]

Hi Fabian

As far as I know, the way to send your contribution is contacting 
someone who administrate the website. I think Justin is one of them.


Probably some of them are reading us and can help you.

Cheers

--
Prof. Dr. Alexandre Suman de Araujo
Departamento de Física
Instituto de Biociências, Letras e Ciências Exatas - IBILCE
Universidade Estadual Paulista
e-mail: asara...@ibilce.unesp.br
Phone: +55 (17) 3221-2566/3221-2240


Em 25-08-2011 13:18, Fabian Casteblanco escreveu:

Hello Dr. Alexandre Suman de Araujo,

I am not sure how to upload to Gromacs User Contribution.  I see
downloadable files but not place to upload.  Do you have the link
where I can upload the files?

Thanks,
Fabian

On Wed, Aug 24, 2011 at 2:55 PM, Fabian Casteblanco
  wrote:

Hello Steven Neumann,

I recently converted CGenFF parameters into files that are used by
Gromacs.  If this is what you need, shoot me an email and I can
provide you with the data sets.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com





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[gmx-users] Re: Convert drug Charmm topology to Gromacs

[Fabian Casteblanco]

Hello Dr. Alexandre Suman de Araujo,

I am not sure how to upload to Gromacs User Contribution.  I see
downloadable files but not place to upload.  Do you have the link
where I can upload the files?

Thanks,
Fabian

On Wed, Aug 24, 2011 at 2:55 PM, Fabian Casteblanco
 wrote:
> Hello Steven Neumann,
>
> I recently converted CGenFF parameters into files that are used by
> Gromacs.  If this is what you need, shoot me an email and I can
> provide you with the data sets.
>
> --
> Best regards,
>
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering PhD Student
> C: +908 917 0723
> E:  fabian.castebla...@gmail.com
>



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
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Re: [gmx-users] Obtaining protein structure

[Steven Neumann]

Thank you for your help. I want to calculate binging free energy of small
molecules to protein termini.

Steven

On Thu, Aug 25, 2011 at 4:22 PM, Mark Abraham wrote:

>  On 26/08/2011 1:16 AM, Steven Neumann wrote:
>
> Dear Gromacs Users,
>
> I want to do some simulations of the protein (its N anc C terminals) which
> crystal structure does not exist.
>
>
> There will normally be reasons why the termini do not have a defined
> structure - often that this are in fact disordered. That will make your life
> doing simulations considerably more difficult, and not just in choosing a
> starting structure.
>
>
>  I submitted the sequence to www.proteinmodelportal.org obtaining
> different structures based on different proteins from Protein Data Bank. For
> instance my N terminal has 180 aa. Obtained models covers %Seq id of 78% for
> 36 residues, 68% for 36 different residues, 62% of 36 another residues and
> many other models below 50%. The website provides you with the PDB files of
> your query so sounds perfect as you do not have to mutate every residue one
> by one.
> The question is whether this is efficent and provide a good result to use
> such protein in my simualtions? Is this app. too big?
>
>
> Depends what simulations you plan - but very likely you will not be able to
> study more than one or two candidate structures.
>
>
>  What are the other ways to overcome this problem (obtain structure of the
> protein which crystal structure does not exist?
>
>
> Protein structure prediction is a field all of its own for a reason. It's
> hard.
>
> Mark
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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[gmx-users] g_wham issue

[chris . neale]

Please provide very much more information. Unless somebody has run  
into the exact thing that you are describing it is currently  
impossible for us to help you.


One thing I can suggest now is to construct histograms of the sampling  
from the coord.xvg files yourself with some scripting and plot them  
all together to see if you have some regions with no overlap (but even  
still, please address my first point).


-- original message --

Hi all:

I have been trying to figure out a problem in our umbrella sampling  
simulation. We are simulating a coarse grained protein passing through  
a coarse grained lipid bilayer. In the pull simulation, the protein  
was made to move from +z=6 nm of the box through the lipid layer at  
z=0 to z= -4 nm. For umbrella sampling 74 windows where chosen with a  
0.2 nm. When we look at the histogram from  the g_wham, we get good  
overlap before the protein touches the bilayer and after it has exited  
the bilayer. We also get the PMF curves for these regions.


However, when the the protein is in contact, and barely touching the  
bilayer, the g_wham analysis gives 0.000E+0 for PMF and no histograms  
in the output. We have tried decreasing the window size from 0.2 to  
0.1 nm but it does not help.


I looked at the gmx-user list to find a possible solution to this  
issue but could not find any helpful clue. Could anyone point me to  
what should be done and what is possibly going wrong?


Thanks,
SNC
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Re: [gmx-users] Obtaining protein structure

[Mark Abraham]

On 26/08/2011 1:16 AM, Steven Neumann wrote:

Dear Gromacs Users,
I want to do some simulations of the protein (its N anc C terminals) 
which crystal structure does not exist.


There will normally be reasons why the termini do not have a defined 
structure - often that this are in fact disordered. That will make your 
life doing simulations considerably more difficult, and not just in 
choosing a starting structure.


I submitted the sequence to www.proteinmodelportal.org 
 obtaining different structures 
based on different proteins from Protein Data Bank. For instance my N 
terminal has 180 aa. Obtained models covers %Seq id of 78% for 36 
residues, 68% for 36 different residues, 62% of 36 another residues 
and many other models below 50%. The website provides you with the PDB 
files of your query so sounds perfect as you do not have to mutate 
every residue one by one.
The question is whether this is efficent and provide a good result to 
use such protein in my simualtions? Is this app. too big?


Depends what simulations you plan - but very likely you will not be able 
to study more than one or two candidate structures.


What are the other ways to overcome this problem (obtain structure of 
the protein which crystal structure does not exist?


Protein structure prediction is a field all of its own for a reason. 
It's hard.


Mark
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Re: [gmx-users] Obtaining protein structure

[Justin A. Lemkul]

Steven Neumann wrote:

Dear Gromacs Users,
 
I want to do some simulations of the protein (its N anc C terminals) 
which crystal structure does not exist. I submitted the sequence to 
www.proteinmodelportal.org  
obtaining different structures based on different proteins from Protein 
Data Bank. For instance my N terminal has 180 aa. Obtained models covers 
%Seq id of 78% for 36 residues, 68% for 36 different residues, 62% of 36 
another residues and many other models below 50%. The website provides 
you with the PDB files of your query so sounds perfect as you do not 
have to mutate every residue one by one.
The question is whether this is efficent and provide a good result to 
use such protein in my simualtions? Is this app. too big?
What are the other ways to overcome this problem (obtain structure of 
the protein which crystal structure does not exist?
 


Homology modeling is a field unto itself.  There are many programs that produce 
results with varying accuracy.  A quick look through some of the documentation 
from that site suggests there should be good feedback about the quality of the 
model.


There are probably other forums better suited to these types of discussions. 
This mailing list is intended for Gromacs-related issues and usage.  Please bear 
that in mind.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Obtaining protein structure

[Steven Neumann]

Dear Gromacs Users,

I want to do some simulations of the protein (its N anc C terminals) which
crystal structure does not exist. I submitted the sequence to
www.proteinmodelportal.org obtaining different structures based on different
proteins from Protein Data Bank. For instance my N terminal has 180 aa.
Obtained models covers %Seq id of 78% for 36 residues, 68% for 36 different
residues, 62% of 36 another residues and many other models below 50%. The
website provides you with the PDB files of your query so sounds perfect as
you do not have to mutate every residue one by one.
The question is whether this is efficent and provide a good result to use
such protein in my simualtions? Is this app. too big?
What are the other ways to overcome this problem (obtain structure of the
protein which crystal structure does not exist?

Thank you in advance,

Steven
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[gmx-users] g_wham issue

[shikha nangia]

Hi all: 

I have been trying to figure out a problem in our umbrella sampling simulation. 
We are simulating a coarse grained protein passing through a coarse grained 
lipid bilayer. In the pull simulation, the protein was made to move from +z=6 
nm of the box through the lipid layer at z=0 to z= -4 nm. For umbrella sampling 
74 windows where chosen with a 0.2 nm. When we look at the histogram from  the 
g_wham, we get good overlap before the protein touches the bilayer and after it 
has exited the bilayer. We also get the PMF curves for these regions.

However, when the the protein is in contact, and barely touching the bilayer, 
the g_wham analysis gives 0.000E+0 for PMF and no histograms in the output. We 
have tried decreasing the window size from 0.2 to 0.1 nm but it does not help. 

I looked at the gmx-user list to find a possible solution to this issue but 
could not find any helpful clue. Could anyone point me to what should be done 
and what is possibly going wrong?

Thanks,
SNC
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Re: [gmx-users] Convert drug Charmm topology to Gromacs

[Alexandre Suman de Araujo]

Why don't you post this in User Contribution area of Gromacs Website?

I think this is something that could interest a lot of people.

Cheers

--
Prof. Dr. Alexandre Suman de Araujo
Departamento de Física
Instituto de Biociências, Letras e Ciências Exatas - IBILCE
Universidade Estadual Paulista
e-mail: asara...@ibilce.unesp.br
Phone: +55 (17) 3221-2566/3221-2240


Em 24-08-2011 15:55, Fabian Casteblanco escreveu:

Hello Steven Neumann,

I recently converted CGenFF parameters into files that are used by
Gromacs.  If this is what you need, shoot me an email and I can
provide you with the data sets.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com

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Re: [gmx-users] Difficulty building a topology for a synthetic branched PEG-peptide molecule

[Mark Abraham]

On 25/08/2011 3:10 AM, Pablo Englebienne wrote:

Hi all,

I am trying to build a topology for a synthetic molecule that consists 
of peptides connected by oligoethyleneglycol (I'll call it PEG) 
linkers terminated with an amine and a carboxylic acid:


-NH2-CH2-[CH2-O-CH2]n-CH2-C(=O)-

The system looks like this:

N-(PEG)-C-N-(peptide2)-Lys(C-ter)-NZ-C-(PEG)-N

So:
* the C-terminus of a PEG linker is attached to the N terminus of the 
peptide
* the terminal Lys on the peptide is attached to the C-terminus of a 
PEG linker


I was able to successfully build a topology for this molecule by:
* defining appropriate residues (for the PEG chains and the Lys with a 
PEG attached on the NZ) in a local copy of the forcefield file, adding 
the residues' topologies to aminoacids.rtp
* using the specbond.dat file to define the bond between the NZ in the 
Lys and the PEG linker

* adding the residues to residuetypes.dat with a "Protein" type
* calling pdb2gmx with the -ter option to assign the protonation states

Now, I need to extend the topology to a molecule like this one:

N-(peptide1)-C-N-(PEG)-C-N-(peptide2)-Lys(C-ter)-NZ-C-(PEG)-N-C-(peptide3)-N 



The difficulty with this molecule is that it has 2 N-termini and a 
single C-terminus (in the Lys with the PEG attached to the NZ 
sidechain). pdb2gmx recognizes the whole molecule as a peptide, but 
treats the last residue as a C-terminus, when it actually is an 
N-terminus.


I found in the description for specbond.dat 
(http://www.gromacs.org/Documentation/File_Formats/specbond.dat) that 
for a branched peptide the "-chainsep" option of pdb2gmx can be used, 
so I started to work on that. I split the molecules in 2 chains like 
this:


N-(peptide1)-C-N-(PEG)-C-N-(peptide2)-Lys(C-ter)-NZ- || 
-C-(PEG)-N-C-(peptide3)-N


I reversed the order of the residues in the second chain, so that the 
residues are in N-to-C order. With this, pdb2gmx recognizes the proper 
termini when called as:


$ pdb2gmx -f substrate_edited-reversed.pdb -ter -chainsep interactive

I tried setting the protonation of the termini as charged for the 
"real" termini and None for the artificial one (the one that should be 
handled by specbond.dat), but I get an error message:


---[pdb2gmx output]---
[...]
Splitting PDB chains based on TER records or changing chain id.
Merge chain ending with residue LYSS27 (chain id ' ', atom 71 NZ) with
chain starting with residue GLU28 (chain id 'p', atom 308 OE2)? [n/y]
n

Merged 1 chains into one molecule definition

There are 2 chains and 0 blocks of water and 47 residues with 303 atoms

  chain  #res #atoms
  1 ' '27198
  2 'p'17105
[...]
Identified residue ARG1 as a starting terminus.
Identified residue LYSS27 as a ending terminus.
9 out of 9 lines of specbond.dat converted successfully
Special Atom Distance matrix:
  PEA118
  CG1125
  LYSS27   NZ198   2.762


That's a long bond. Does your reference length in specbond.dat suit it? 
IIRC there should be some evidence in the output of the special bond 
being formed if it actually is. If not, your symptoms are probably related.


Oh, and well done for constructing a good question. You would likely not 
have gotten anywhere giving less detail :)


Mark


Select start terminus type for ARG-1
 0: NH3+
 1: NH2
 2: None
0
Start terminus ARG-1: NH3+
Select end terminus type for LYSS-27
 0: COO-
 1: COOH
 2: None
0
End terminus LYSS-27: COO-
[...]
Identified residue GLU28 as a starting terminus.
Identified residue PEA47 as a ending terminus.
9 out of 9 lines of specbond.dat converted successfully
Select start terminus type for GLU-28
 0: NH3+
 1: NH2
 2: None
0
Start terminus GLU-28: NH3+
Select end terminus type for PEA-47
 0: COO-
 1: COOH
 2: None
2
End terminus PEA-47: None
[...]
---
Program pdb2gmx, VERSION 4.5.4
Source code file: pdb2top.c, line: 1035

Fatal error:
There is a dangling bond at at least one of the terminal ends. Select 
a proper terminal entry.
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---
---[pdb2gmx output]---

I think that the problem might stem from the fact that the C-terminus 
in the second chain is not a real peptide; I changed residuetypes.dat 
to have the PEG residues as "Other", which causes pdb2gmx to recognize 
the last aminoacid as a C-terminus, but treating it as "None" yields 
the same error. Unfortunately, there is nothing about this error in 
http://www.gromacs.org/Documentation/Errors .


Any suggestions on how to make this work will be greatly appreciated!



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Antw: Re: Re: Antw: Re: [gmx-users] Hydrogen existence time

[Emanuel Peter]

The number of frames is in your mdp-file.
nstxout = frequency of output (timestep when it writes out one frame)
dt = timestep

time of frame = number_of_frame * nstxout * dt

With programming you have to learn one certain programming-language.
I cannot help you with learning programming - this at least you have to do
yourself.

>>what programming should be applied and what for

I would suggest you to learn C or Fortran-coding.
You also could use a script-language, like bash.
A theoretician must be able to do some little programming. 

If you want to do that 1000.000 times by hand, you can do it.
You also could integrate the equations of motion by hand for your trajectory.

>>> aiswarya pawar  25.08.11 10.54 Uhr >>>
Dear Emanuel,

Thank you so much for the pseudo-code, it made me understand the flow.
from your code it shows that, your using distance and angle as an criteria to
select a water molecule in just one one time frame. right?? i didnt get how to
calculate the time of the frame. what programming should be applied and what
for.

Thanks,
Aiswarya

On Thu, Aug 25, 2011 at 1:53 PM, Emanuel Peter
 wrote:
Hello Aiswarya,

Your program should look like this, in pseudo-code:

pseudo-code:

do n_frames_of_your_trajectory

g_mindist -f traj.trr -s .tpr -n (your_protein (first-group) , your_solvent
(second-group)).ndx -o atm-pair.out -d your-distance-value -b  (one frame of
your trajectory) -e (the same frame)

processing the atm-pair.out list and write them into an index file : 1.ndx,
with each water in one group

take just these atoms  and residues, which are at your specific distance at
your 'location'

do

measure the angle in relation to your protein for this frame for each specified
water 

g_angle  -f traj.trr -s .tpr -n 1.ndx  -b (one frame of your trajectory) -e
(the same frame)

enddo

read the angles from the output

take just the one water with specific angle out of your list.

(By using g_mindist -d , and g_angle  you specify one specific point in
relation to your protein)
(By using -b and -e you specify one specific time)

save the residue number of this water and your frame

calculate the time of this frame 

enddo

now you have an array of residue numbers at this particular location for each
time

analyse this array, then you know the maximum frame-time of one water-molecule
at this specific location.
You will not get any information about one particular time - just an average.
This must be your residence time.

Your application needs some little programming.

>>>  24.08.11 18.14 Uhr >>>
Emanuel,

The residence time which am referring is the water molecule residing on the
particular location at a specific time.

Am not able to write a correct equation due to some character missing when
typing from phone.

Aiswarya
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
From:  aiswarya.pa...@gmail.com
Date: Wed, 24 Aug 2011 16:13:05 +
To: Gromacs mail
ReplyTo:  aiswarya.pa...@gmail.com
Subject: Re: Antw: Re: [gmx-users] Hydrogen existence time


Emanuel,

The residence time which am referring is the water molecule residing on the
particular location at a specific time.

Am not able to write a correct equation due to small character missing when
typing from phone.

Aiswarya
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
From:  "Emanuel Peter" 
Date: Wed, 24 Aug 2011 16:16:37 +0200
To: ; 
Subject: Antw: Re: [gmx-users] Hydrogen existence time


As I told you, you can calculate the self-diffusion coefficient by using g_msd.
Following:

Large diffusion-coeff. --> means : The residence time is low.
Small diffusion-coeff. --> means : The residence time is large 

Mean-square-displacement means: Displacement of molecules per time.
No displacement of molecule at all : if(msd == 0)  means: Infinite residence
time.
So I say from my idiotic point of view: msd ~ residence time ( I still do not
know what you mean with this because
this is usually related to chemical reactors in engineering and NOT in protein
simulation ) 
In your index-file you can index those molecules, which you need.
Your equation does not make sense. 

>>>  24.08.11 16.01 Uhr >>>

Mark,

The residence time equation goes like this-

P(r)= function (N(t) - N(t+r))dt

Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not
equal to 0) ie the site occupied and when x not equal to y or both x and y =0.
N(t) index of water molecule found in the hydration site at time t.


Aiswarya
--Original Message--
From: Mark Abraham
To: Aiswarya Pawar
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 6:09 PM

On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:
> Any idea how can I calculate the residence time of water.

First, seek define what you mean to calculate. If you can't write an 
equation down for it, you can't calculate it.

Mark

Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!




-- 
gmx-users m

Re: Re: Antw: Re: [gmx-users] Hydrogen existence time

[aiswarya pawar]

Dear Emanuel,

Thank you so much for the pseudo-code, it made me understand the flow.
from your code it shows that, your using distance and angle as an criteria
to select a water molecule in just one one time frame. right?? i didnt get
how to calculate the time of the frame. what programming should be applied
and what for.

Thanks,
Aiswarya

On Thu, Aug 25, 2011 at 1:53 PM, Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> wrote:

> Hello Aiswarya,
>
> Your program should look like this, in pseudo-code:
>
> pseudo-code:
>
> do n_frames_of_your_trajectory
>
> g_mindist -f traj.trr -s .tpr -n (your_protein (first-group) , your_solvent
> (second-group)).ndx -o atm-pair.out -d your-distance-value -b  (one frame of
> your trajectory) -e (the same frame)
>
> processing the atm-pair.out list and write them into an index file : 1.ndx,
> with each water in one group
>
> take just these atoms  and residues, which are at your specific distance at
> your 'location'
>
> do
>
> measure the angle in relation to your protein for this frame for each
> specified water
>
> g_angle  -f traj.trr -s .tpr -n 1.ndx  -b (one frame of your trajectory) -e
> (the same frame)
>
> enddo
>
> read the angles from the output
>
> take just the one water with specific angle out of your list.
>
> (By using g_mindist -d , and g_angle  you specify one specific point in
> relation to your protein)
> (By using -b and -e you specify one specific time)
>
> save the residue number of this water and your frame
>
> calculate the time of this frame
>
> enddo
>
> now you have an array of residue numbers at this particular location for
> each time
>
> analyse this array, then you know the maximum frame-time of one
> water-molecule at this specific location.
> You will not get any information about one particular time - just an
> average.
> This must be your residence time.
>
> Your application needs some little programming.
>
>
> >>> ** 24.08.11 18.14 Uhr >>>
> Emanuel,
>
> The residence time which am referring is the water molecule residing on the
> particular location at a specific time.
>
> Am not able to write a correct equation due to some character missing when
> typing from phone.
>
> Aiswarya
>
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
> it!
> --
> *From: * aiswarya.pa...@gmail.com
> *Date: *Wed, 24 Aug 2011 16:13:05 +
> *To: *Gromacs mail
> *ReplyTo: * aiswarya.pa...@gmail.com
> *Subject: *Re: Antw: Re: [gmx-users] Hydrogen existence time
>
> Emanuel,
>
> The residence time which am referring is the water molecule residing on the
> particular location at a specific time.
>
> Am not able to write a correct equation due to small character missing when
> typing from phone.
>
> Aiswarya
>
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
> it!
> --
> *From: * "Emanuel Peter" 
> *Date: *Wed, 24 Aug 2011 16:16:37 +0200
> *To: *; 
> *Subject: *Antw: Re: [gmx-users] Hydrogen existence time
>
> As I told you, you can calculate the self-diffusion coefficient by using
> g_msd.
> Following:
>
> Large diffusion-coeff. --> means : The residence time is low.
> Small diffusion-coeff. --> means : The residence time is large 
>
> Mean-square-displacement means: Displacement of molecules per time.
> No displacement of molecule at all : if(msd == 0)  means: Infinite
> residence time.
> So I say from my idiotic point of view: msd ~ residence time ( I still do
> not know what you mean with this because
> this is usually related to chemical reactors in engineering and NOT in
> protein simulation )
> In your index-file you can index those molecules, which you need.
> Your equation does not make sense.
>
> >>>  24.08.11 16.01 Uhr >>>
> Mark,
>
> The residence time equation goes like this-
>
> P(r)= function (N(t) - N(t+r))dt
>
> Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y
> not equal to 0) ie the site occupied and when x not equal to y or both x and
> y =0. N(t) index of water molecule found in the hydration site at time t.
>
> Aiswarya
> --Original Message--
> From: Mark Abraham
> To: Aiswarya Pawar
> Subject: Re: [gmx-users] Hydrogen existence time
> Sent: 24 Aug 2011 6:09 PM
>
> On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:
> > Any idea how can I calculate the residence time of water.
>
> First, seek define what you mean to calculate. If you can't write an
> equation down for it, you can't calculate it.
>
> Mark
>
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
> it!**
>
-- 
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Please search the archive at 
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Antw: Re: Antw: Re: [gmx-users] Hydrogen existence time

[Emanuel Peter]

Hello Aiswarya,

Your program should look like this, in pseudo-code:

pseudo-code:

do n_frames_of_your_trajectory

g_mindist -f traj.trr -s .tpr -n (your_protein (first-group) , your_solvent
(second-group)).ndx -o atm-pair.out -d your-distance-value -b  (one frame of
your trajectory) -e (the same frame)

processing the atm-pair.out list and write them into an index file : 1.ndx,
with each water in one group

take just these atoms  and residues, which are at your specific distance at
your 'location'

do

measure the angle in relation to your protein for this frame for each specified
water 

g_angle  -f traj.trr -s .tpr -n 1.ndx  -b (one frame of your trajectory) -e
(the same frame)

enddo

read the angles from the output

take just the one water with specific angle out of your list.

(By using g_mindist -d , and g_angle  you specify one specific point in
relation to your protein)
(By using -b and -e you specify one specific time)

save the residue number of this water and your frame

calculate the time of this frame 

enddo

now you have an array of residue numbers at this particular location for each
time

analyse this array, then you know the maximum frame-time of one water-molecule
at this specific location.
You will not get any information about one particular time - just an average.
This must be your residence time.

Your application needs some little programming.

>>>  24.08.11 18.14 Uhr >>>
Emanuel,

The residence time which am referring is the water molecule residing on the
particular location at a specific time.

Am not able to write a correct equation due to some character missing when
typing from phone.

AiswaryaSent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go
for it!
From:  aiswarya.pa...@gmail.com
Date: Wed, 24 Aug 2011 16:13:05 +
To: Gromacs mail
ReplyTo:  aiswarya.pa...@gmail.com
Subject: Re: Antw: Re: [gmx-users] Hydrogen existence time


Emanuel,

The residence time which am referring is the water molecule residing on the
particular location at a specific time.

Am not able to write a correct equation due to small character missing when
typing from phone.

AiswaryaSent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go
for it!
From:  "Emanuel Peter" 
Date: Wed, 24 Aug 2011 16:16:37 +0200
To: ; 
Subject: Antw: Re: [gmx-users] Hydrogen existence time


As I told you, you can calculate the self-diffusion coefficient by using g_msd.
Following:

Large diffusion-coeff. --> means : The residence time is low.
Small diffusion-coeff. --> means : The residence time is large 

Mean-square-displacement means: Displacement of molecules per time.
No displacement of molecule at all : if(msd == 0)  means: Infinite residence
time.
So I say from my idiotic point of view: msd ~ residence time ( I still do not
know what you mean with this because
this is usually related to chemical reactors in engineering and NOT in protein
simulation ) 
In your index-file you can index those molecules, which you need.
Your equation does not make sense. 

>>>  24.08.11 16.01 Uhr >>>
Mark,

The residence time equation goes like this-

P(r)= function (N(t) - N(t+r))dt

Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not
equal to 0) ie the site occupied and when x not equal to y or both x and y =0.
N(t) index of water molecule found in the hydration site at time t.

Aiswarya
--Original Message--
From: Mark Abraham
To: Aiswarya Pawar
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 6:09 PM

On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:
> Any idea how can I calculate the residence time of water.

First, seek define what you mean to calculate. If you can't write an 
equation down for it, you can't calculate it.

Mark

Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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