Re: [gmx-users] Ion pair

2017-09-07 Thread David van der Spoel 

On 07/09/17 03:38, Tuanan Lourenço wrote:

Hi everybody,

I am working with electrolytes simulations using Gromacs, so I am trying to
get the residence time (ion pair lifetime, ion cage lifetime) of the ions.
I tried to use gmx hbond with the option -contat, but if try get the acf of
the interaction the program always has a crash, I also have tried Travis
package, but the ACFs does not look nice in this application. So I am tring
to write my own code for this analysis but I have a dead line coming soon,
if some one know about a program in which I can do this analysis I will be
very glad.

Thank you

We just used this analysis recently so it should work. You don't say 
which gromacs version you are using, but in the most recent it should be 
fine as far as I know.


--
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[gmx-users] Running multiple Gromacs simulations on the same node

2017-09-07 Thread MING HA 
Hi all,


It may seem a bit weird, but I'm trying to run multiple Gromacs simulations
simultaneously on the same node, and I specified each Gromacs simulation
to use only 1 MPI process and 1 OMP thread. I'm doing this because I am
trying to check how accurate my model can predict an application using a
single thread and process.

My question is: If, for example, I am running multiple Gromacs simulations
simultaneously, each with 1 MPI process and 1 OMP thread,  on the same
node, does each simulation use separate MPI processes and OMP threads,
or are they shared?


Sincerely,
Ming
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Re: [gmx-users] Ion pair

2017-09-07 Thread André Farias de Moura 
Hi Tuanan,

although it's not a distributable/documented code, I have an old Fortran
program (dating back to my PhD days) that does just that.

Please feel free to contact me off the list if you think it might be of any
use to you.

best

André

On Wed, Sep 6, 2017 at 10:38 PM, Tuanan Lourenço 
wrote:

> Hi everybody,
>
> I am working with electrolytes simulations using Gromacs, so I am trying to
> get the residence time (ion pair lifetime, ion cage lifetime) of the ions.
> I tried to use gmx hbond with the option -contat, but if try get the acf of
> the interaction the program always has a crash, I also have tried Travis
> package, but the ACFs does not look nice in this application. So I am tring
> to write my own code for this analysis but I have a dead line coming soon,
> if some one know about a program in which I can do this analysis I will be
> very glad.
>
> Thank you
>
> --
> __
> MSc. Tuanan C Lourenço
> Ph.D Student Physical Chemistry - Universidade Federal Fluminense
> Molecular Modelling and Computer Simullation Group - UFF
> MOLMOD-CS WEBSITE 
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_

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Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 161, Issue 20

2017-09-07 Thread Justin Lemkul 



On 9/7/17 4:09 PM, vijayakumar gosu wrote:

I have used below mdrun command

taskset -c 0-79 gmx mdrun -deffnm md_0_1 -v

i am not sure whether i have to apply mpi threads.



To communicate between nodes, yes.  Be sure you read 
http://www.gromacs.org/Documentation/Acceleration_and_parallelization to 
understand the parallelization schemes in GROMACS and make best use of your 
resources.


-Justin

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==

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Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 161, Issue 20

2017-09-07 Thread vijayakumar gosu 
I have used below mdrun command

taskset -c 0-79 gmx mdrun -deffnm md_0_1 -v

i am not sure whether i have to apply mpi threads.





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> Today's Topics:
>
>1. Re: Incorrect link for release notes of gromacs 2016.3
>   (Szil?rd P?ll)
>2. Diffusion coefficient (Sohaib. Mohammed)
>3. Re: Merging different topology files (Justin Lemkul)
>4. Re: purpose of step pdb files during MD (Justin Lemkul)
>5. gromacs installation (vijayakumar gosu)
>6. Re: gromacs installation (Wes Barnett)
>
>
> --
>
> Message: 1
> Date: Thu, 7 Sep 2017 18:59:24 +0200
> From: Szil?rd P?ll 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] Incorrect link for release notes of gromacs
> 2016.3
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Fixed it, thanks ?ke!
> --
> Szil?rd
>
>
> On Thu, Sep 7, 2017 at 6:36 PM, ?ke Sandgren 
> wrote:
> > Hi!
> >
> > The link for the release notes of gromacs 2016.3 on www.gromacs.org is
> > pointing to 2016.1
> >
> > --
> > Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> > Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
> > Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
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> --
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> Message: 2
> Date: Thu, 7 Sep 2017 14:07:57 -0500
> From: "Sohaib. Mohammed" 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Diffusion coefficient
> Message-ID:
>  mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hey Users,
>
> I want to calculate the diffusion coefficient using gmx msd. I want to
> divide the box into slices of 5 A parallel to z axis and calculate the
> diffusion coefficient for each slice. My question is how to make these
> slices, I've tried gmx trajconv but didn't work with me. I believe it's
> quite simple and provided by gromacs, but I am struggling with it.
> Appreciate any idea on how to make these slices.
>
> Thank you,
> Sohaib
>
>
> --
>
> Message: 3
> Date: Thu, 7 Sep 2017 15:08:49 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Merging different topology files
> Message-ID: <2b8ad61e-73e4-75fe-7e1f-195376985...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 9/7/17 10:19 AM, Momin Ahmad wrote:
> > Hello all,
> >
> > is there a simple way to merge two or more topology files into one? I
> > am trying to use grompp to set up a simulation but my solvation
> > contains different molecules which have different .top files. I also
> > tried creating a main topology file which includes the other two
> > topologies but without success. Hope anyone knows how to solve this.
> >
>
> The #include mechanism is the only way to do this.? If you have two .top
> (system topology) files, then:
>
> 1. Remove any #include statement for a parent force field (i.e. the file
> with [defaults] in it)
> 2. Remove any [system] or [molecules] directive
>
> (you now have proper .itp format)
>
> 3. Remove any redundant #include statements (e.g. for water, ions) to
> avoid "moleculetype redefined" errors
> 4. Construct a new .top that #includes a parent force field, your two
> new .itp files, and has [system] and [molecules] directives.
>
> -Justin
>
> --
>
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://

Re: [gmx-users] gromacs installation

2017-09-07 Thread Wes Barnett 
On Thu, Sep 7, 2017 at 3:25 PM, vijayakumar gosu 
wrote:

> Hi,
>
> I have installed gromacs 5.1 in server which has 4 nodes each with 40 cpus.
> I am allotted to use only 2 nodes with 80 cpus. after installation when i
> did sample md run only 20 cpus are being utilized. How can I fully utilize
> the all 80 CPUs for mdrun.
>
> I have used below cmake command for the installation
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF
> -DREGRESSIONTEST_PATH=/BiO/BioTools/regressiontests-5.1.1 -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> -DCMAKE_INSTALL_PREFIX=/Bio/BioTools/gromacs
>
> I have not seen any errors during installation.
>

You should go ahead and just install 2016.3 instead of 5.1.

What is your exact command when you run mdrun?

-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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[gmx-users] gromacs installation

2017-09-07 Thread vijayakumar gosu 
Hi,

I have installed gromacs 5.1 in server which has 4 nodes each with 40 cpus.
I am allotted to use only 2 nodes with 80 cpus. after installation when i
did sample md run only 20 cpus are being utilized. How can I fully utilize
the all 80 CPUs for mdrun.

I have used below cmake command for the installation

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF
-DREGRESSIONTEST_PATH=/BiO/BioTools/regressiontests-5.1.1 -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
-DCMAKE_INSTALL_PREFIX=/Bio/BioTools/gromacs

I have not seen any errors during installation.

Thanks.
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Re: [gmx-users] purpose of step pdb files during MD

2017-09-07 Thread Justin Lemkul 



On 9/7/17 10:29 AM, Vedat Durmaz wrote:

i really appreciate this pretty informative answer. and do you also know, what the infix 
"n254" or "n2" stands for?


Node ID.


what i found strange is that the error occurs after nearly 10M MD steps. in 
other copies of the same system, the error doesn't occur at all even after the 
entire predefines time span (40ns).

it's a long fibril chain (>200 repeating units) of a 7mer polypeptide. the walls of the 
triclinic simulation box of size 10x8x70 nm have an initial distance of 1.5 nm to the fibril 
and i have chosen "comm-mode  = linear" in order to keep the system centered. i'm 
actually wondering, whether that might have caused the error or whether the system will for 
sure crash if the long chain changes its shape to some spheric one that doesn't fit the slim 
box anymore.

do you have any experience with that?


Nope, sorry.  A crash after a long simulation time is very unusual and 
hard to diagnose.  Normally things fail rather quickly.  Does your 
GROMACS installation pass all regression tests?


-Justin

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Virginia Tech Department of Biochemistry

303 Engel Hall
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Re: [gmx-users] Merging different topology files

2017-09-07 Thread Justin Lemkul 



On 9/7/17 10:19 AM, Momin Ahmad wrote:

Hello all,

is there a simple way to merge two or more topology files into one? I 
am trying to use grompp to set up a simulation but my solvation 
contains different molecules which have different .top files. I also 
tried creating a main topology file which includes the other two 
topologies but without success. Hope anyone knows how to solve this.




The #include mechanism is the only way to do this.  If you have two .top 
(system topology) files, then:


1. Remove any #include statement for a parent force field (i.e. the file 
with [defaults] in it)

2. Remove any [system] or [molecules] directive

(you now have proper .itp format)

3. Remove any redundant #include statements (e.g. for water, ions) to 
avoid "moleculetype redefined" errors
4. Construct a new .top that #includes a parent force field, your two 
new .itp files, and has [system] and [molecules] directives.


-Justin

--

==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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[gmx-users] Diffusion coefficient

2017-09-07 Thread Sohaib. Mohammed 
Hey Users,

I want to calculate the diffusion coefficient using gmx msd. I want to
divide the box into slices of 5 A parallel to z axis and calculate the
diffusion coefficient for each slice. My question is how to make these
slices, I've tried gmx trajconv but didn't work with me. I believe it's
quite simple and provided by gromacs, but I am struggling with it.
Appreciate any idea on how to make these slices.

Thank you,
Sohaib
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Re: [gmx-users] Incorrect link for release notes of gromacs 2016.3

2017-09-07 Thread Szilárd Páll 
Fixed it, thanks Åke!
--
Szilárd


On Thu, Sep 7, 2017 at 6:36 PM, Åke Sandgren  wrote:
> Hi!
>
> The link for the release notes of gromacs 2016.3 on www.gromacs.org is
> pointing to 2016.1
>
> --
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
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[gmx-users] Incorrect link for release notes of gromacs 2016.3

2017-09-07 Thread Åke Sandgren 
Hi!

The link for the release notes of gromacs 2016.3 on www.gromacs.org is
pointing to 2016.1

-- 
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Re: [gmx-users] purpose of step pdb files during MD

2017-09-07 Thread Vedat Durmaz 

i really appreciate this pretty informative answer. and do you also know, what 
the infix "n254" or "n2" stands for?

what i found strange is that the error occurs after nearly 10M MD steps. in 
other copies of the same system, the error doesn't occur at all even after the 
entire predefines time span (40ns).

it's a long fibril chain (>200 repeating units) of a 7mer polypeptide. the 
walls of the triclinic simulation box of size 10x8x70 nm have an initial 
distance of 1.5 nm to the fibril and i have chosen "comm-mode  = linear" in 
order to keep the system centered. i'm actually wondering, whether that might 
have caused the error or whether the system will for sure crash if the long 
chain changes its shape to some spheric one that doesn't fit the slim box 
anymore.

do you have any experience with that?

vedat



Am 07.09.2017 um 14:26 schrieb Justin Lemkul:
>
> On 9/6/17 5:55 AM, Vedat Durmaz wrote:
>> hi guys,
>>
>> from time to time i'm faced with GMX output files during MD called, e.g. in 
>> the current case:
>>
>> step8164372b_n254.pdb
>> step8164372b_n2.pdb
>> step8164372c_n254.pdb
>> step8164372c_n2.pdb
>>
>> what i know is that they are related to kind of exploding systems. however, 
>> i'm not really able to interpret their content. if i visualize them in VMD, 
>> i see a subset of my system surounded by explicit water molecules where the 
>> two *n254* files contain a larger part of my fibrils (polypeptides) than the 
>> *n2* files which only show few atoms of one particular amino acid. but if i 
>> pick certain atoms of the amino acids, they are often not correctly assigned 
>> to residue names and the atom index shown in VMD is different from the index 
>> listed in the underlying gro file.
>>
>> where can i find detailed information about how to interpret the names and 
>> contents of these files? why are exactly these atoms written to the pdb 
>> files and what does the file name tell me?
> These files contain the atoms in a given domain (e.g. on a certain CPU 
> core) and are before (b) and after (c) applying constraints of a given 
> step.  I personally have never found them to be useful in determining 
> anything, but they are an indicator of physical instability.
>
> -Justin
>


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[gmx-users] Fwd: Merging different topology files

2017-09-07 Thread Momin Ahmad 

weird, my email got cut off



 Weitergeleitete Nachricht 
Betreff:Merging different topology files
Datum:  Thu, 7 Sep 2017 16:19:29 +0200
Von:Momin Ahmad 
An: gmx-us...@gromacs.org



Hello all,

is there a simple way to merge two or more topology files into one? I am
trying to use grompp to set up a simulation but my solvation contains
different molecules which have different .top files. I also tried
creating a main topology file which includes the other two topologies
but without success. Hope anyone knows how to solve this.

Best,
Momin

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[gmx-users] Merging different topology files

2017-09-07 Thread Momin Ahmad 

Hello all,

is there a simple way to merge two or more topology files into one? I am 
trying to use grompp to set up a simulation but my solvation contains 
different molecules which have different .top files. I also tried 
creating a main topology file which includes the other two topologies 
but without success. Hope anyone knows how to solve this.


Best,
Momin
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Re: [gmx-users] gromacs ligand topology file for "GNP"

2017-09-07 Thread Justin Lemkul 



On 9/7/17 9:23 AM, Deep kumar wrote:

Hello,

On Thu, Sep 7, 2017 at 1:11 AM, Justin Lemkul  wrote:



On 9/6/17 3:46 PM, Deep kumar wrote:


Dear All,

I have produced the "ITP" files of the ligands using ATB server.  I am
mentioning the steps here, please let me know if you think anything is
wrong.

a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.

b) Entered the "net charge" by calculating like this using chimera: (added
Hydrogen prior to calculating net charge and produced .mol2 file to
calculate the net charge)

from chimera import openModels, Molecule
from AddCharge import estimateNetCharge
from OpenSave import osOpen
output = osOpen("charge-estimates", "w")
for m in openModels.list(modelTypes=[Molecule]):
  print>>output, m, m.name, estimateNetCharge(m.atoms)
output.close()

the "net charge" of "RND" was shown to be "2".



Does that make sense?  What is RND?


RND is the ligand found in 4NYM.pdb file. I am trying to make a system of
this pdb for MD.



I understand that; I'm trying to get you to think a little bit about the 
chemistry.  What are the titratable groups and what are their pKa 
values?  Does a +2 net charge make sense?  This would be pretty uncommon 
for any small molecule that is considered an inhibitor/ligand for a protein.




c) submitted the entry and after completion, downloaded the file as below:

  From "Molecular Dynamics(MD) files", chose "Forcefield" to be
"Gromos54A7"
& "Format" to be "Gromacs", and downloaded "All Atom" ITP file.

I am running the MD on Gromacs version 5.1. I have prepared the protein
topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.

Please let me know if I did right or if anything else is needed to be
done.

Secondly, I also need .gro file of the ligand. Can you please let me know
how can I get that. The tutorial am following (
http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I
have to prepare a position restraint file "posre_RND.itp" from the
"RND.gro" file, so how can I get the "RND.gro" file?



You don't need a .gro file to generate a position restraint file; as with
most operations in GROMACS, you can use any coordinate file format here.
If you *really* want to use .gro, you can transform between formats with
editconf.

And lastly, please let me know how to generate topology of "GNP" molecule

with gromos53A6 FF. I tried ATB but it says error "
Error recorded: Unsupported bond length encountered: 0.56nm (PA-O5'). This
often indicates there is an error in the submitted structure.
"



The error here is pretty clear.  You have a bad geometry for this molecule
with a bond length that is about 3 times longer than it really should be.
Visualizing the coordinates should make this apparent since ATB is telling
you exactly which bond is problematic.


Thanks, can you please let me know how can I solve this problem?


Look at the geometry - is there a problem?  Has the PDB file you're 
supplying for GNP been modified in any way?  Does it visualize 
properly?  I doubt an experimental assignment of a 0.56-nm bond would be 
made when it should be on the order of 0.16 nm or so.


-Justin




-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] gromacs ligand topology file for "GNP"

2017-09-07 Thread Deep kumar 
Hello,

On Thu, Sep 7, 2017 at 1:11 AM, Justin Lemkul  wrote:

>
>
> On 9/6/17 3:46 PM, Deep kumar wrote:
>
>> Dear All,
>>
>> I have produced the "ITP" files of the ligands using ATB server.  I am
>> mentioning the steps here, please let me know if you think anything is
>> wrong.
>>
>> a) uploaded the coordinates of ligand "RND" on ATB server. I chose
>> "heteromoelcule" molecule type.
>>
>> b) Entered the "net charge" by calculating like this using chimera: (added
>> Hydrogen prior to calculating net charge and produced .mol2 file to
>> calculate the net charge)
>>
>> from chimera import openModels, Molecule
>> from AddCharge import estimateNetCharge
>> from OpenSave import osOpen
>> output = osOpen("charge-estimates", "w")
>> for m in openModels.list(modelTypes=[Molecule]):
>>  print>>output, m, m.name, estimateNetCharge(m.atoms)
>> output.close()
>>
>> the "net charge" of "RND" was shown to be "2".
>>
>>
> Does that make sense?  What is RND?


RND is the ligand found in 4NYM.pdb file. I am trying to make a system of
this pdb for MD.


>
>
> c) submitted the entry and after completion, downloaded the file as below:
>>
>>  From "Molecular Dynamics(MD) files", chose "Forcefield" to be
>> "Gromos54A7"
>> & "Format" to be "Gromacs", and downloaded "All Atom" ITP file.
>>
>> I am running the MD on Gromacs version 5.1. I have prepared the protein
>> topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.
>>
>> Please let me know if I did right or if anything else is needed to be
>> done.
>>
>> Secondly, I also need .gro file of the ligand. Can you please let me know
>> how can I get that. The tutorial am following (
>> http://www.bevanlab.biochem.
>> vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I
>> have to prepare a position restraint file "posre_RND.itp" from the
>> "RND.gro" file, so how can I get the "RND.gro" file?
>>
>>
> You don't need a .gro file to generate a position restraint file; as with
> most operations in GROMACS, you can use any coordinate file format here.
> If you *really* want to use .gro, you can transform between formats with
> editconf.
>
> And lastly, please let me know how to generate topology of "GNP" molecule
>> with gromos53A6 FF. I tried ATB but it says error "
>> Error recorded: Unsupported bond length encountered: 0.56nm (PA-O5'). This
>> often indicates there is an error in the submitted structure.
>> "
>>
>>
> The error here is pretty clear.  You have a bad geometry for this molecule
> with a bond length that is about 3 times longer than it really should be.
> Visualizing the coordinates should make this apparent since ATB is telling
> you exactly which bond is problematic.
>

Thanks, can you please let me know how can I solve this problem?


>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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>
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Re: [gmx-users] DPOSRES not working

2017-09-07 Thread Sergio Manzetti 
I cant say I fancy one who wants make money on knowing what on other peoples 
mind, but that does not mean you are the same! :) 

I think this worked out, but what the "bug" may be, that after doing 5 
simulations twice, each time the confout.gro is something different from the 
confout.gro that came out afterwards from using gmx trjconv maybe something 
irrelated and related to linux command line/rights etc? 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Thursday, September 7, 2017 3:02:10 PM 
Subject: Re: [gmx-users] DPOSRES not working 

On 9/7/17 8:52 AM, Sergio Manzetti wrote: 
> Hey Justin , you sound like Mark Zuckerberg :) 

I don't know whether that's good or bad... 

> Here is the command I used: 
> 
> gmx trjconv -f traj -o confout5000.gro -b 1 -e 1 

-dump 1 is easier than using -b and -e, FYI. 

> 
> and it gives the write gro with DNA in the box as it should be. 

So then things worked, yes? 

> This confout.gro is not the same as came out from the GMX run, at the same 
> moment as the TRJ and XTC came 

In what way? Why does this lead you to believe that your restraints 
aren't working? The questions I asked before are more diagnostic of 
whether or not things are functioning. Dumping a (non-PBC-corrected) 
frame and looking at another one (PBC corrected, albeit perhaps not in 
the best way) does not say anything about whether or not the algorithms 
are working. 

-Justin 

> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | 
> FAP ] 
> 
> 
> 
> From: "Justin Lemkul"  
> To: "gmx-users"  
> Sent: Thursday, September 7, 2017 2:55:05 PM 
> Subject: Re: [gmx-users] DPOSRES not working 
> 
> On 9/7/17 8:45 AM, Sergio Manzetti wrote: 
>> It seems that GMX simply didn't write out the correct frame. The confout.gro 
>> file written out is written at the same time as the trajectories, and for 
>> some reason, this confout.gro file has nothing to do with the last output 
>> frame from the sims, when produced by gmx trjconv.. 
> confout.gro is the final frame, re-wrapped for PBC. So it may "look" 
> different from the final frame of the trajectory, but it's not. 
> 
> Unless you actually provide answers to the questions I asked and any 
> actual commands you're issuing (e.g. what did you do when you say 
> "produced by gmx trjconv" for instance?), then there's nothing anyone 
> here can do to help you. We can't see what you're seeing or interpret 
> what's in your mind :) 
> 
> -Justin 
> 
>> 
>> 
>> 
>> 
>> Sergio Manzetti 
>> 
>> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
>> 
>> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | 
>> ] 
>> Midtun 
>> 6894 Vangsnes 
>> Norge 
>> Org.nr. 911 659 654 
>> Tlf: +47 57695621 
>> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
>> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | 
>> FAP ] 
>> 
>> 
>> 
>> From: "Justin Lemkul"  
>> To: "gmx-users"  
>> Sent: Thursday, September 7, 2017 2:28:23 PM 
>> Subject: Re: [gmx-users] DPOSRES not working 
>> 
>> On 9/7/17 5:28 AM, Sergio Manzetti wrote: 
>>> Hi Johannes, yes, they are there in both cases: 
>>> 
>>> ; Include Position restraint file 
>>> #ifdef POSRES 
>>> #include "posre_DNA_chain_E.itp" 
>>> #endif 
>>> 
>> Do you have a position restraint energy term written in your .log file, 
>> and if so, what is its magnitude? Does your DNA start at the middle of 
>> the box (GROMACS convention) or at the coordinate origin (like other 
>> software)? If you watch the trajectory evolve, what happens? Does the 
>> DNA move a lot or does it just bounce back and forth around its original 
>> position (suggesting your box is simply too small and any time an atom 
>> crosses a boundary, you get a jump)? 
>> 
>> -Justin 
>> 

-- 
== 

Justin A. Lemkul, Ph.D. 
Assistant Professor 
Virginia Tech Department of Biochemistry 

303 Engel Hall 
340 West Campus Dr. 
Blacksburg, VA 24061 

jalem...@vt.edu | (540) 231-3129 
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html 

== 

-- 
Gromacs Users mailing list 

* Please search the archive at 
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Re: [gmx-users] DPOSRES not working

2017-09-07 Thread Justin Lemkul 



On 9/7/17 8:52 AM, Sergio Manzetti wrote:

Hey Justin , you sound like Mark Zuckerberg :)


I don't know whether that's good or bad...


Here is the command I used:

gmx trjconv -f traj -o confout5000.gro -b 1 -e 1


-dump 1 is easier than using -b and -e, FYI.



and it gives the write gro with DNA in the box as it should be.


So then things worked, yes?


This confout.gro is not the same as came out from the GMX run, at the same 
moment as the TRJ and XTC came


In what way?  Why does this lead you to believe that your restraints 
aren't working?  The questions I asked before are more diagnostic of 
whether or not things are functioning.  Dumping a (non-PBC-corrected) 
frame and looking at another one (PBC corrected, albeit perhaps not in 
the best way) does not say anything about whether or not the algorithms 
are working.


-Justin



Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ]



From: "Justin Lemkul" 
To: "gmx-users" 
Sent: Thursday, September 7, 2017 2:55:05 PM
Subject: Re: [gmx-users] DPOSRES not working

On 9/7/17 8:45 AM, Sergio Manzetti wrote:

It seems that GMX simply didn't write out the correct frame. The confout.gro 
file written out is written at the same time as the trajectories, and for some 
reason, this confout.gro file has nothing to do with the last output frame from 
the sims, when produced by gmx trjconv..

confout.gro is the final frame, re-wrapped for PBC. So it may "look"
different from the final frame of the trajectory, but it's not.

Unless you actually provide answers to the questions I asked and any
actual commands you're issuing (e.g. what did you do when you say
"produced by gmx trjconv" for instance?), then there's nothing anyone
here can do to help you. We can't see what you're seeing or interpret
what's in your mind :)

-Justin






Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory 
] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ]



From: "Justin Lemkul" 
To: "gmx-users" 
Sent: Thursday, September 7, 2017 2:28:23 PM
Subject: Re: [gmx-users] DPOSRES not working

On 9/7/17 5:28 AM, Sergio Manzetti wrote:

Hi Johannes, yes, they are there in both cases:

; Include Position restraint file
#ifdef POSRES
#include "posre_DNA_chain_E.itp"
#endif


Do you have a position restraint energy term written in your .log file,
and if so, what is its magnitude? Does your DNA start at the middle of
the box (GROMACS convention) or at the coordinate origin (like other
software)? If you watch the trajectory evolve, what happens? Does the
DNA move a lot or does it just bounce back and forth around its original
position (suggesting your box is simply too small and any time an atom
crosses a boundary, you get a jump)?

-Justin



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] DPOSRES not working

2017-09-07 Thread Sergio Manzetti 
Hey Justin , you sound like Mark Zuckerberg :) 

Here is the command I used: 

gmx trjconv -f traj -o confout5000.gro -b 1 -e 1 


and it gives the write gro with DNA in the box as it should be. 

This confout.gro is not the same as came out from the GMX run, at the same 
moment as the TRJ and XTC came 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Thursday, September 7, 2017 2:55:05 PM 
Subject: Re: [gmx-users] DPOSRES not working 

On 9/7/17 8:45 AM, Sergio Manzetti wrote: 
> It seems that GMX simply didn't write out the correct frame. The confout.gro 
> file written out is written at the same time as the trajectories, and for 
> some reason, this confout.gro file has nothing to do with the last output 
> frame from the sims, when produced by gmx trjconv.. 

confout.gro is the final frame, re-wrapped for PBC. So it may "look" 
different from the final frame of the trajectory, but it's not. 

Unless you actually provide answers to the questions I asked and any 
actual commands you're issuing (e.g. what did you do when you say 
"produced by gmx trjconv" for instance?), then there's nothing anyone 
here can do to help you. We can't see what you're seeing or interpret 
what's in your mind :) 

-Justin 

> 
> 
> 
> 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | 
> FAP ] 
> 
> 
> 
> From: "Justin Lemkul"  
> To: "gmx-users"  
> Sent: Thursday, September 7, 2017 2:28:23 PM 
> Subject: Re: [gmx-users] DPOSRES not working 
> 
> On 9/7/17 5:28 AM, Sergio Manzetti wrote: 
>> Hi Johannes, yes, they are there in both cases: 
>> 
>> ; Include Position restraint file 
>> #ifdef POSRES 
>> #include "posre_DNA_chain_E.itp" 
>> #endif 
>> 
> Do you have a position restraint energy term written in your .log file, 
> and if so, what is its magnitude? Does your DNA start at the middle of 
> the box (GROMACS convention) or at the coordinate origin (like other 
> software)? If you watch the trajectory evolve, what happens? Does the 
> DNA move a lot or does it just bounce back and forth around its original 
> position (suggesting your box is simply too small and any time an atom 
> crosses a boundary, you get a jump)? 
> 
> -Justin 
> 

-- 
== 

Justin A. Lemkul, Ph.D. 
Assistant Professor 
Virginia Tech Department of Biochemistry 

303 Engel Hall 
340 West Campus Dr. 
Blacksburg, VA 24061 

jalem...@vt.edu | (540) 231-3129 
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html 

== 

-- 
Gromacs Users mailing list 

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! 

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 

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Re: [gmx-users] DPOSRES not working

2017-09-07 Thread Justin Lemkul 



On 9/7/17 8:45 AM, Sergio Manzetti wrote:

It seems that GMX simply didn't write out the correct frame. The confout.gro 
file written out is written at the same time as the trajectories, and for some 
reason, this confout.gro file has nothing to do with the last output frame from 
the sims, when produced by gmx trjconv..


confout.gro is the final frame, re-wrapped for PBC.  So it may "look" 
different from the final frame of the trajectory, but it's not.


Unless you actually provide answers to the questions I asked and any 
actual commands you're issuing (e.g. what did you do when you say 
"produced by gmx trjconv" for instance?), then there's nothing anyone 
here can do to help you.  We can't see what you're seeing or interpret 
what's in your mind :)


-Justin







Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ]



From: "Justin Lemkul" 
To: "gmx-users" 
Sent: Thursday, September 7, 2017 2:28:23 PM
Subject: Re: [gmx-users] DPOSRES not working

On 9/7/17 5:28 AM, Sergio Manzetti wrote:

Hi Johannes, yes, they are there in both cases:

; Include Position restraint file
#ifdef POSRES
#include "posre_DNA_chain_E.itp"
#endif


Do you have a position restraint energy term written in your .log file,
and if so, what is its magnitude? Does your DNA start at the middle of
the box (GROMACS convention) or at the coordinate origin (like other
software)? If you watch the trajectory evolve, what happens? Does the
DNA move a lot or does it just bounce back and forth around its original
position (suggesting your box is simply too small and any time an atom
crosses a boundary, you get a jump)?

-Justin



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] DPOSRES not working

2017-09-07 Thread Sergio Manzetti 
It seems that GMX simply didn't write out the correct frame. The confout.gro 
file written out is written at the same time as the trajectories, and for some 
reason, this confout.gro file has nothing to do with the last output frame from 
the sims, when produced by gmx trjconv.. 






Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Thursday, September 7, 2017 2:28:23 PM 
Subject: Re: [gmx-users] DPOSRES not working 

On 9/7/17 5:28 AM, Sergio Manzetti wrote: 
> Hi Johannes, yes, they are there in both cases: 
> 
> ; Include Position restraint file 
> #ifdef POSRES 
> #include "posre_DNA_chain_E.itp" 
> #endif 
> 

Do you have a position restraint energy term written in your .log file, 
and if so, what is its magnitude? Does your DNA start at the middle of 
the box (GROMACS convention) or at the coordinate origin (like other 
software)? If you watch the trajectory evolve, what happens? Does the 
DNA move a lot or does it just bounce back and forth around its original 
position (suggesting your box is simply too small and any time an atom 
crosses a boundary, you get a jump)? 

-Justin 

-- 
== 

Justin A. Lemkul, Ph.D. 
Assistant Professor 
Virginia Tech Department of Biochemistry 

303 Engel Hall 
340 West Campus Dr. 
Blacksburg, VA 24061 

jalem...@vt.edu | (540) 231-3129 
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html 

== 

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Re: [gmx-users] DPOSRES not working

2017-09-07 Thread Justin Lemkul 



On 9/7/17 5:28 AM, Sergio Manzetti wrote:

Hi Johannes, yes, they are there in both cases:

; Include Position restraint file
#ifdef POSRES
#include "posre_DNA_chain_E.itp"
#endif



Do you have a position restraint energy term written in your .log file, 
and if so, what is its magnitude?  Does your DNA start at the middle of 
the box (GROMACS convention) or at the coordinate origin (like other 
software)?  If you watch the trajectory evolve, what happens?  Does the 
DNA move a lot or does it just bounce back and forth around its original 
position (suggesting your box is simply too small and any time an atom 
crosses a boundary, you get a jump)?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] purpose of step pdb files during MD

2017-09-07 Thread Justin Lemkul 



On 9/6/17 5:55 AM, Vedat Durmaz wrote:

hi guys,

from time to time i'm faced with GMX output files during MD called, e.g. in the 
current case:

step8164372b_n254.pdb
step8164372b_n2.pdb
step8164372c_n254.pdb
step8164372c_n2.pdb

what i know is that they are related to kind of exploding systems. however, i'm 
not really able to interpret their content. if i visualize them in VMD, i see a 
subset of my system surounded by explicit water molecules where the two *n254* 
files contain a larger part of my fibrils (polypeptides) than the *n2* files 
which only show few atoms of one particular amino acid. but if i pick certain 
atoms of the amino acids, they are often not correctly assigned to residue 
names and the atom index shown in VMD is different from the index listed in the 
underlying gro file.

where can i find detailed information about how to interpret the names and 
contents of these files? why are exactly these atoms written to the pdb files 
and what does the file name tell me?


These files contain the atoms in a given domain (e.g. on a certain CPU 
core) and are before (b) and after (c) applying constraints of a given 
step.  I personally have never found them to be useful in determining 
anything, but they are an indicator of physical instability.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] selecting atoms in index file

2017-09-07 Thread G R 
On Thu, Sep 7, 2017 at 12:35 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
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>
>
> Today's Topics:
>
>1. Re: selecting atoms in index file (Hermann, Johannes)
>2. Re: DPOSRES not working (Hermann, Johannes)
>3. Re: DPOSRES not working (Sergio Manzetti)
>4. Re: DPOSRES not working (Hermann, Johannes)
>5. Re: DPOSRES not working (Sergio Manzetti)
>
>
> --
>
> Message: 1
> Date: Thu, 7 Sep 2017 11:16:08 +0200
> From: "Hermann, Johannes" 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] selecting atoms in index file
> Message-ID: 
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear Golnaz,
>
> do you know the number (index) of the respective atoms? E.g. open the
> .gro file in vmd and look for the atoms?
>
> If there are not too many atoms, you can manually edit your index file.
> E.g. create a default index file (gmx make_ndx) and add the subset of
> indexes with a new selection definition:
>
> ---
>
> [ MySelection]
>
> 23 57 75
>
> ---
>
> All the best
>
> Johannes
>
> Hi Johanne,
>
> Thank you for your reply. just one more question: when I edit atoms in my
> index file, should I delete these atoms from surfaces groups. let me
> explain better. Now I have 2 groups in my index file Sol and
> Kaoli(surface). I should select some atoms from the Kaoli. So first I
> define the atoms that I want to select in a seperate group, then I should
> erase these atoms from kaoli parts. Am I right?  because I want to freeze
> the surface without these atoms.
>
> On 07.09.2017 11:02, G R wrote:
> > Dear All,
> >
> > I want to create an index file and select some especial atoms in a
> surface.
> > My problem is that I have only one residue for the whole surface. How
> can I
> > select the atoms on the surface as a different groups in my index file?
> >
> > Thank you in advance,
> > Golnaz
>
> --
> __
> *Technische Universit?t M?nchen*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl f?r Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: j.herm...@lrz.tum.de
> http://www.biovt.mw.tum.de/
>
>
>
> --
>
> Message: 2
> Date: Thu, 7 Sep 2017 11:18:29 +0200
> From: "Hermann, Johannes" 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] DPOSRES not working
> Message-ID: <8c01673e-77d8-fa16-c5ad-ec0269a47...@lrz.tum.de>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear Sergio,
>
> how did you define the position restrain in your topology? Check your
> topology and position restrain file.
>
> All the best
>
> Johannes
>
>
> On 07.09.2017 11:07, Sergio Manzetti wrote:
> > Hello, I am running 5 simulations with the given mdp:
> >
> > title = DNA in water stabilization
> > cpp = /lib/cpp
> > include = -I../top
> > define = -DPOSRES
> > integrator = md
> > dt = 0.002
> > nsteps = 1000
> > nstxout = 5000
> > nstvout = 5000
> > nstlog = 5000
> > nstenergy = 300
> > nstxout-compressed = 300
> > compressed-x-grps = PRB SOL NA CL DNA
> > energygrps = PRB SOL NA CL DNA
> > nstlist = 10
> > ns-type = grid
> > rlist = 0.8
> > coulombtype = PME
> > rcoulomb = 0.8
> > rvdw = 0.8
> > tcoupl = V-Rescale
> > tc-grps = System
> > tau-t = 0.1
> > ref-t = 310
> > Pcoupl = No
> > tau-p = 1.0
> > compressibility = 4.5e-5
> > ref-p = 1.0
> > gen-vel = yes
> > gen-temp = 310
> > gen-seed = 17527
> > constraints = all-bonds
> >
> >
> > and still, the DNA splits into two
> >
> > Any ideas what could be wrong?
> >
> > Thanks
> >
> > Sergio Manzetti
> >
> > [ http://www.fjordforsk.no/logo_hr2.jpg ]
> >
> > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [
> http://www.fjordforsk.no/ |   ]
> > Midtun
> > 6894 Vangsnes
> > Norge
> > Org.nr. 911 659 654
> > Tlf: +47 57695621
> > [ http://www.oekolab.com/ | ?kolab  ] | [ http://www.nanofact.no/ |
> Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [
> http://www.phap.no/ | FAP ]
> >
>
> --
> __
> *Technische Universit?t M?nchen*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl f?r Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: j.herm...@lrz.tum.de
> http://www.biovt.mw.tum.de/
>
>
>
> --
>
> Message: 3
> Date: Thu, 7 Sep 2017 11:15

Re: [gmx-users] DPOSRES not working

2017-09-07 Thread Sergio Manzetti 
Hi Johannes, yes, they are there in both cases: 

; Include Position restraint file 
#ifdef POSRES 
#include "posre_DNA_chain_E.itp" 
#endif 



Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Hermann, Johannes"  
To: "gmx-users"  
Sent: Thursday, September 7, 2017 11:29:03 AM 
Subject: Re: [gmx-users] DPOSRES not working 

Okay, but what did you define in your topologies for your DNA chains: 

#include "topol_DNA_chain_E.itp" 
#include "topol_DNA_chain_F.itp" 

Make sure that at the end of these files you have lines stating e.g: 

; Include Position restraint file 
#ifdef POSRES 
#include "posre_DNA_chain_E.itp" 
#endif 

The same for your other chain. 

Normally pdb2gmx creats a position restrain file posre_DNA_chain_E.itp 
for all the heavy atoms. If you do not have this position restrain file 
you can generate it with gmx genrestr. 

Last but not least you can read about position restrains in the manual. 

All the best 
Johannes 


On 07.09.2017 11:15, Sergio Manzetti wrote: 
> Hi Johannes, it appears so: 
> 
> 
> ; Include forcefield parameters 
> #include "amber99sb-ildn.ff/forcefield.itp" 
> 
> ; Include chain topologies 
> #include "topol_DNA_chain_E.itp" 
> #include "topol_DNA_chain_F.itp" 
> #include "PRB_GMX.itp" 
> 
> ; Include water topology 
> #include "amber99sb-ildn.ff/spc.itp" 
> 
> #ifdef POSRES_WATER 
> ; Position restraint for each water oxygen 
> [ position_restraints ] 
> ; i funct fcx fcy fcz 
> 1 1 1000 1000 1000 
> #endif 
> 
> ; Include topology for ions 
> #include "amber99sb-ildn.ff/ions.itp" 
> 
> [ system ] 
> ; Name 
> CRYSTAL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA in water 
> 
> [ molecules ] 
> ; Compound #mols 
> DNA_chain_E 1 
> DNA_chain_F 1 
> NA 71 
> CL 31 
> PRB 1 
> SOL 16349 
> 
> 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | 
> FAP ] 
> 
> 
> 
> From: "Hermann, Johannes"  
> To: "gmx-users"  
> Sent: Thursday, September 7, 2017 11:18:29 AM 
> Subject: Re: [gmx-users] DPOSRES not working 
> 
> Dear Sergio, 
> 
> how did you define the position restrain in your topology? Check your 
> topology and position restrain file. 
> 
> All the best 
> 
> Johannes 
> 
> 
> On 07.09.2017 11:07, Sergio Manzetti wrote: 
>> Hello, I am running 5 simulations with the given mdp: 
>> 
>> title = DNA in water stabilization 
>> cpp = /lib/cpp 
>> include = -I../top 
>> define = -DPOSRES 
>> integrator = md 
>> dt = 0.002 
>> nsteps = 1000 
>> nstxout = 5000 
>> nstvout = 5000 
>> nstlog = 5000 
>> nstenergy = 300 
>> nstxout-compressed = 300 
>> compressed-x-grps = PRB SOL NA CL DNA 
>> energygrps = PRB SOL NA CL DNA 
>> nstlist = 10 
>> ns-type = grid 
>> rlist = 0.8 
>> coulombtype = PME 
>> rcoulomb = 0.8 
>> rvdw = 0.8 
>> tcoupl = V-Rescale 
>> tc-grps = System 
>> tau-t = 0.1 
>> ref-t = 310 
>> Pcoupl = No 
>> tau-p = 1.0 
>> compressibility = 4.5e-5 
>> ref-p = 1.0 
>> gen-vel = yes 
>> gen-temp = 310 
>> gen-seed = 17527 
>> constraints = all-bonds 
>> 
>> 
>> and still, the DNA splits into two 
>> 
>> Any ideas what could be wrong? 
>> 
>> Thanks 
>> 
>> Sergio Manzetti 
>> 
>> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
>> 
>> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | 
>> ] 
>> Midtun 
>> 6894 Vangsnes 
>> Norge 
>> Org.nr. 911 659 654 
>> Tlf: +47 57695621 
>> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
>> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | 
>> FAP ] 
>> 

-- 
__ 
*Technische Universität München* 
*Johannes Hermann, M.Sc.* 
Lehrstuhl für Bioverfahrenstechnik 
Boltzmannstr. 15 
D-85748 Garching 
Tel: +49 8928915730 
Fax: +49 8928915714 

Email: j.herm...@lrz.tum.de 
http://www.biovt.mw.tum.de/ 

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* For (un)subsc

Re: [gmx-users] DPOSRES not working

2017-09-07 Thread Hermann, Johannes 

Okay, but what did you define in your topologies for your DNA chains:

#include "topol_DNA_chain_E.itp"
#include "topol_DNA_chain_F.itp"

Make sure that at the end of these files you have lines stating e.g:

; Include Position restraint file
#ifdef POSRES
#include "posre_DNA_chain_E.itp"
#endif

The same for your other chain.

Normally pdb2gmx creats a position restrain file posre_DNA_chain_E.itp 
for all the heavy atoms. If you do not have this position restrain file 
you can generate it with gmx genrestr.


Last but not least you can read about position restrains in the manual.

All the best
Johannes


On 07.09.2017 11:15, Sergio Manzetti wrote:

Hi Johannes, it appears so:


; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"

; Include chain topologies
#include "topol_DNA_chain_E.itp"
#include "topol_DNA_chain_F.itp"
#include "PRB_GMX.itp"

; Include water topology
#include "amber99sb-ildn.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include "amber99sb-ildn.ff/ions.itp"

[ system ]
; Name
CRYSTAL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA in water

[ molecules ]
; Compound #mols
DNA_chain_E 1
DNA_chain_F 1
NA 71
CL 31
PRB 1
SOL 16349



Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ]



From: "Hermann, Johannes" 
To: "gmx-users" 
Sent: Thursday, September 7, 2017 11:18:29 AM
Subject: Re: [gmx-users] DPOSRES not working

Dear Sergio,

how did you define the position restrain in your topology? Check your
topology and position restrain file.

All the best

Johannes


On 07.09.2017 11:07, Sergio Manzetti wrote:

Hello, I am running 5 simulations with the given mdp:

title = DNA in water stabilization
cpp = /lib/cpp
include = -I../top
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 1000
nstxout = 5000
nstvout = 5000
nstlog = 5000
nstenergy = 300
nstxout-compressed = 300
compressed-x-grps = PRB SOL NA CL DNA
energygrps = PRB SOL NA CL DNA
nstlist = 10
ns-type = grid
rlist = 0.8
coulombtype = PME
rcoulomb = 0.8
rvdw = 0.8
tcoupl = V-Rescale
tc-grps = System
tau-t = 0.1
ref-t = 310
Pcoupl = No
tau-p = 1.0
compressibility = 4.5e-5
ref-p = 1.0
gen-vel = yes
gen-temp = 310
gen-seed = 17527
constraints = all-bonds


and still, the DNA splits into two

Any ideas what could be wrong?

Thanks

Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory 
] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ]



--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] DPOSRES not working

2017-09-07 Thread Sergio Manzetti 
Hi Johannes, it appears so: 


; Include forcefield parameters 
#include "amber99sb-ildn.ff/forcefield.itp" 

; Include chain topologies 
#include "topol_DNA_chain_E.itp" 
#include "topol_DNA_chain_F.itp" 
#include "PRB_GMX.itp" 

; Include water topology 
#include "amber99sb-ildn.ff/spc.itp" 

#ifdef POSRES_WATER 
; Position restraint for each water oxygen 
[ position_restraints ] 
; i funct fcx fcy fcz 
1 1 1000 1000 1000 
#endif 

; Include topology for ions 
#include "amber99sb-ildn.ff/ions.itp" 

[ system ] 
; Name 
CRYSTAL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA in water 

[ molecules ] 
; Compound #mols 
DNA_chain_E 1 
DNA_chain_F 1 
NA 71 
CL 31 
PRB 1 
SOL 16349 



Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
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Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
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 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Hermann, Johannes"  
To: "gmx-users"  
Sent: Thursday, September 7, 2017 11:18:29 AM 
Subject: Re: [gmx-users] DPOSRES not working 

Dear Sergio, 

how did you define the position restrain in your topology? Check your 
topology and position restrain file. 

All the best 

Johannes 


On 07.09.2017 11:07, Sergio Manzetti wrote: 
> Hello, I am running 5 simulations with the given mdp: 
> 
> title = DNA in water stabilization 
> cpp = /lib/cpp 
> include = -I../top 
> define = -DPOSRES 
> integrator = md 
> dt = 0.002 
> nsteps = 1000 
> nstxout = 5000 
> nstvout = 5000 
> nstlog = 5000 
> nstenergy = 300 
> nstxout-compressed = 300 
> compressed-x-grps = PRB SOL NA CL DNA 
> energygrps = PRB SOL NA CL DNA 
> nstlist = 10 
> ns-type = grid 
> rlist = 0.8 
> coulombtype = PME 
> rcoulomb = 0.8 
> rvdw = 0.8 
> tcoupl = V-Rescale 
> tc-grps = System 
> tau-t = 0.1 
> ref-t = 310 
> Pcoupl = No 
> tau-p = 1.0 
> compressibility = 4.5e-5 
> ref-p = 1.0 
> gen-vel = yes 
> gen-temp = 310 
> gen-seed = 17527 
> constraints = all-bonds 
> 
> 
> and still, the DNA splits into two 
> 
> Any ideas what could be wrong? 
> 
> Thanks 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | 
> FAP ] 
> 

-- 
__ 
*Technische Universität München* 
*Johannes Hermann, M.Sc.* 
Lehrstuhl für Bioverfahrenstechnik 
Boltzmannstr. 15 
D-85748 Garching 
Tel: +49 8928915730 
Fax: +49 8928915714 

Email: j.herm...@lrz.tum.de 
http://www.biovt.mw.tum.de/ 

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Re: [gmx-users] DPOSRES not working

2017-09-07 Thread Hermann, Johannes 

Dear Sergio,

how did you define the position restrain in your topology? Check your 
topology and position restrain file.


All the best

Johannes


On 07.09.2017 11:07, Sergio Manzetti wrote:

Hello, I am running 5 simulations with the given mdp:

title = DNA in water stabilization
cpp = /lib/cpp
include = -I../top
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 1000
nstxout = 5000
nstvout = 5000
nstlog = 5000
nstenergy = 300
nstxout-compressed = 300
compressed-x-grps = PRB SOL NA CL DNA
energygrps = PRB SOL NA CL DNA
nstlist = 10
ns-type = grid
rlist = 0.8
coulombtype = PME
rcoulomb = 0.8
rvdw = 0.8
tcoupl = V-Rescale
tc-grps = System
tau-t = 0.1
ref-t = 310
Pcoupl = No
tau-p = 1.0
compressibility = 4.5e-5
ref-p = 1.0
gen-vel = yes
gen-temp = 310
gen-seed = 17527
constraints = all-bonds


and still, the DNA splits into two

Any ideas what could be wrong?

Thanks

Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ]



--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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Re: [gmx-users] selecting atoms in index file

2017-09-07 Thread Hermann, Johannes 

Dear Golnaz,

do you know the number (index) of the respective atoms? E.g. open the 
.gro file in vmd and look for the atoms?


If there are not too many atoms, you can manually edit your index file. 
E.g. create a default index file (gmx make_ndx) and add the subset of 
indexes with a new selection definition:


---

[ MySelection]

23 57 75

---

All the best

Johannes


On 07.09.2017 11:02, G R wrote:

Dear All,

I want to create an index file and select some especial atoms in a surface.
My problem is that I have only one residue for the whole surface. How can I
select the atoms on the surface as a different groups in my index file?

Thank you in advance,
Golnaz


--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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[gmx-users] DPOSRES not working

2017-09-07 Thread Sergio Manzetti 
Hello, I am running 5 simulations with the given mdp: 

title = DNA in water stabilization 
cpp = /lib/cpp 
include = -I../top 
define = -DPOSRES 
integrator = md 
dt = 0.002 
nsteps = 1000 
nstxout = 5000 
nstvout = 5000 
nstlog = 5000 
nstenergy = 300 
nstxout-compressed = 300 
compressed-x-grps = PRB SOL NA CL DNA 
energygrps = PRB SOL NA CL DNA 
nstlist = 10 
ns-type = grid 
rlist = 0.8 
coulombtype = PME 
rcoulomb = 0.8 
rvdw = 0.8 
tcoupl = V-Rescale 
tc-grps = System 
tau-t = 0.1 
ref-t = 310 
Pcoupl = No 
tau-p = 1.0 
compressibility = 4.5e-5 
ref-p = 1.0 
gen-vel = yes 
gen-temp = 310 
gen-seed = 17527 
constraints = all-bonds 


and still, the DNA splits into two 

Any ideas what could be wrong? 

Thanks 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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[gmx-users] selecting atoms in index file

2017-09-07 Thread G R 
Dear All,

I want to create an index file and select some especial atoms in a surface.
My problem is that I have only one residue for the whole surface. How can I
select the atoms on the surface as a different groups in my index file?

Thank you in advance,
Golnaz
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Re: [gmx-users] purpose of step pdb files during MD

2017-09-07 Thread Vytautas Rakeviius 
Energy minimization output explains them. I do not think they are important if 
you get good energy minimization after all.
 

On Thursday, September 7, 2017, 3:41:59 AM GMT+3, Vedat Durmaz 
 wrote:  
 
 
hi guys,

from time to time i'm faced with GMX output files during MD called, e.g. in the 
current case:

step8164372b_n254.pdb
step8164372b_n2.pdb
step8164372c_n254.pdb
step8164372c_n2.pdb

what i know is that they are related to kind of exploding systems. however, i'm 
not really able to interpret their content. if i visualize them in VMD, i see a 
subset of my system surounded by explicit water molecules where the two *n254* 
files contain a larger part of my fibrils (polypeptides) than the *n2* files 
which only show few atoms of one particular amino acid. but if i pick certain 
atoms of the amino acids, they are often not correctly assigned to residue 
names and the atom index shown in VMD is different from the index listed in the 
underlying gro file.

where can i find detailed information about how to interpret the names and 
contents of these files? why are exactly these atoms written to the pdb files 
and what does the file name tell me?

any hint is appreciated.

many thanks,

vedat durmaz


-- 
Vedat Durmaz
Computational Molecular Design
Zuse Institute Berlin (ZIB)
Takustrasse 7
14195 Berlin, Germany
T: +49-30-84185-139
F: +49-30-84185-107
http://www.zib.de/durmaz

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