Re: [gmx-users] Molecular dynamics with LEGO?

[Tsjerk Wassenaar]

Hi James,

There are models, yes. But if a manufacturer like LEGO is taking this up,
it can make the models much cheaper and more easily available. In addition,
the LEGO models would allow more flexibility in building and handling. And
you can combine it with your other LEGO ;)

And, yes, bendy pieces should be next :D Already thought of those.

Cheers,

Tsjerk


On Fri, Oct 18, 2013 at 8:50 PM,  wrote:

> Hi Tsjerk,
>
> In my opinion, we don't need to develop LEGO specifically for this -
> something already exists, which I played with in school. The molymod
> pieces (http://www.molymod.com/) already include bendy pieces, which are
> the next step on the lego website you advertise.
>
> Best wishes
> James
>
> > Hi :)
> >
> > Apologies if this seems inappropriate, but I would like to ask as many
> > people as I can to give support for the molecular modeling LEGO project
> at
> > http://lego.cuusoo.com/ideas/view/51273. With 10 000 votes, LEGO will
> > consider producing the bricks required for such models, and we can add
> > cool
> > a way of modeling to our toolbox.
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
>
>
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Re: [gmx-users] Molecular dynamics with LEGO?

[jkrieger]

Hi Tsjerk,

In my opinion, we don't need to develop LEGO specifically for this -
something already exists, which I played with in school. The molymod
pieces (http://www.molymod.com/) already include bendy pieces, which are
the next step on the lego website you advertise.

Best wishes
James

> Hi :)
>
> Apologies if this seems inappropriate, but I would like to ask as many
> people as I can to give support for the molecular modeling LEGO project at
> http://lego.cuusoo.com/ideas/view/51273. With 10 000 votes, LEGO will
> consider producing the bricks required for such models, and we can add
> cool
> a way of modeling to our toolbox.
>
> Cheers,
>
> Tsjerk
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> 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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>


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[gmx-users] Molecular dynamics with LEGO?

[Tsjerk Wassenaar]

Hi :)

Apologies if this seems inappropriate, but I would like to ask as many
people as I can to give support for the molecular modeling LEGO project at
http://lego.cuusoo.com/ideas/view/51273. With 10 000 votes, LEGO will
consider producing the bricks required for such models, and we can add cool
a way of modeling to our toolbox.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
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[gmx-users] modification of LJ potential

[Zuzana Benkova]

Dear GROMACS users,I went through the mailing list but I am still not sure about my problem. I am going to simulate two chains in a tube using GROMACS. The chains are modeled as strings of connected beads and I would like to describe the interaction with the tube aligned with z axis and passing through [0,0,0] by and additional term to LJ potential in which the r=R-sqrt(x^2+y^2); R is the radius of a tube.I want to simulate this system without pbc. Could you be so kind and give me advice which files of the source code should I modify? Thank you in advance.GreetingsZuzana
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Re: [gmx-users] Problem with reading AMBER trajectories

[Mark Abraham]

OK. All GROMACS does is feed your filename extension to the VMD library and
let it choose how to read the file based on that. If that doesn't make
sense (and it seems it doesn't, because GROMACS wasn't told about the
number of atoms, and it needs to know), then the ball is back to you to
choose the filename extension in the way the plugin needs. I suggest you
check out http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/ and try some
alternatives.

Mark


On Fri, Oct 18, 2013 at 2:10 PM, anu chandra  wrote:

> Hi Mark,
>
> Yes. I do can able to load the trajectories successfully in VMD with the
> file format option of ' AMBER coordinate with periodic box'. I am using VMD
> 1.9 version.
>
> Regards
> Anu
>
>
>
>
> On Fri, Oct 18, 2013 at 1:05 PM, Mark Abraham  >wrote:
>
> > Can this file be opened in VMD itself?
> >
> > Mark
> > On Oct 18, 2013 6:21 AM, "anu chandra"  wrote:
> >
> > > Dear Gromacs users,
> > >
> > > I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing
> > few
> > > analysis. Unfortunately I ended-up with the following error.
> > >
> > > 
> > > GROMACS will now assume it to be a trajectory and will try to open it
> > using
> > > the VMD plug-ins.
> > > This will only work in case the VMD plugins are found and it is a
> > > trajectory format supported by VMD.
> > >
> > > Using VMD plugin: crd (AMBER Coordinates)
> > >
> > > Format of file md.crd does not record number of atoms.
> > >
> > > ---
> > > Program g_covar, VERSION 4.6.1
> > > Source code file: /usr/local/gromacs-4.6.1/src/gmxlib/trxio.c, line:
> 1035
> > >
> > > Fatal error:
> > > Not supported in read_first_frame: md.crd
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > > ---
> > > 
> > >
> > >
> > >
> > > While browsing through the GROMACS mail-list, I came to know that it
> > might
> > > be a problem with DLOPEN libraries. So I recompiled Gromcas with cmake
> > > using the following command
> > >
> > > 
> > > CMAKE_PREFIX_PATH=/usr/include/libltdl cmake
> > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs -DCMAKE_C_COMPILER=gcc
> > > -DCMAKE_CXX_COMPILER=g++ -DFFTWF_LIBRARY=/usr/lib/libfftw3f.a
> > > -DFFTWF_INCLUDE_DIR=/usr/lib/ ../
> > > 
> > >
> > > But, the same problem came-up again. Can anyone help me to figure out
> > what
> > > went wrong with my Gromacs installation?
> > >
> > > Many thanks in advance.
> > >
> > > Regards
> > > Anu
> > > --
> > > 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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> > >
> > --
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> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Bilayer thickness error

[Archana Sonawani-Jagtap]

thank you so much. It was such a stupid error from my side.


On Fri, Oct 18, 2013 at 5:08 PM, Justin Lemkul  wrote:

>
>
> On 10/18/13 2:54 AM, Archana Sonawani-Jagtap wrote:
>
>> Hi,
>> This is my input file for calculating bilayer thickness in absence of
>> peptide:
>> ## Input file and input file parameters
>> coord_file  md.gro
>> file_type gro
>> num_frames   1
>> num_lipid_types1
>> resname1POPC
>> atomname1   P8
>> solvent   SOL
>> ionsCL-
>> ## Define the size and shape of the grid
>> box_sizesolvent
>> grid20
>> conserve_ratioyes
>> ## Define whether there is a protein embedded in the bilayer
>> protein   no
>> precision   1.3
>> P_value 5.0
>> ## Define the desired output files and format
>> output_prefix   output
>> output_format  column
>> thickness   yes
>> area   no
>>
>> I got 400 lines in one column in output file for average thickness
>> (calculated without peptide)
>>
>> When running in Gnuplot I get following error:
>> splot 'output.frame1.20x20.average_**thickness.dat' matrix using
>> (1+$1):(1+$2):3
>> Warning: empty x range [1:1], adjusting to [0.99:1.01]
>>
>>
> Please refer to Appendix A, section 2 of our GridMAT-MD manual, which
> explains the preprocessing necessary to open the file in Gnuplot, otherwise
> refer to the manual section describing the output_format keyword.
>
> You can send GridMAT-MD questions directly to me; there is no need to fill
> peoples' inboxes with non-Gromacs questions.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
> --
> 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/Searchbefore
>  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
>



-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
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Re: [gmx-users] Problem with reading AMBER trajectories

[anu chandra]

Hi Mark,

Yes. I do can able to load the trajectories successfully in VMD with the
file format option of ' AMBER coordinate with periodic box'. I am using VMD
1.9 version.

Regards
Anu




On Fri, Oct 18, 2013 at 1:05 PM, Mark Abraham wrote:

> Can this file be opened in VMD itself?
>
> Mark
> On Oct 18, 2013 6:21 AM, "anu chandra"  wrote:
>
> > Dear Gromacs users,
> >
> > I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing
> few
> > analysis. Unfortunately I ended-up with the following error.
> >
> > 
> > GROMACS will now assume it to be a trajectory and will try to open it
> using
> > the VMD plug-ins.
> > This will only work in case the VMD plugins are found and it is a
> > trajectory format supported by VMD.
> >
> > Using VMD plugin: crd (AMBER Coordinates)
> >
> > Format of file md.crd does not record number of atoms.
> >
> > ---
> > Program g_covar, VERSION 4.6.1
> > Source code file: /usr/local/gromacs-4.6.1/src/gmxlib/trxio.c, line: 1035
> >
> > Fatal error:
> > Not supported in read_first_frame: md.crd
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> > 
> >
> >
> >
> > While browsing through the GROMACS mail-list, I came to know that it
> might
> > be a problem with DLOPEN libraries. So I recompiled Gromcas with cmake
> > using the following command
> >
> > 
> > CMAKE_PREFIX_PATH=/usr/include/libltdl cmake
> > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs -DCMAKE_C_COMPILER=gcc
> > -DCMAKE_CXX_COMPILER=g++ -DFFTWF_LIBRARY=/usr/lib/libfftw3f.a
> > -DFFTWF_INCLUDE_DIR=/usr/lib/ ../
> > 
> >
> > But, the same problem came-up again. Can anyone help me to figure out
> what
> > went wrong with my Gromacs installation?
> >
> > Many thanks in advance.
> >
> > Regards
> > Anu
> > --
> > 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!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
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Re: [gmx-users] Bilayer thickness error

[Justin Lemkul]

On 10/18/13 2:54 AM, Archana Sonawani-Jagtap wrote:

Hi,
This is my input file for calculating bilayer thickness in absence of peptide:
## Input file and input file parameters
coord_file  md.gro
file_type gro
num_frames   1
num_lipid_types1
resname1POPC
atomname1   P8
solvent   SOL
ionsCL-
## Define the size and shape of the grid
box_sizesolvent
grid20
conserve_ratioyes
## Define whether there is a protein embedded in the bilayer
protein   no
precision   1.3
P_value 5.0
## Define the desired output files and format
output_prefix   output
output_format  column
thickness   yes
area   no

I got 400 lines in one column in output file for average thickness
(calculated without peptide)

When running in Gnuplot I get following error:
splot 'output.frame1.20x20.average_thickness.dat' matrix using (1+$1):(1+$2):3
Warning: empty x range [1:1], adjusting to [0.99:1.01]



Please refer to Appendix A, section 2 of our GridMAT-MD manual, which explains 
the preprocessing necessary to open the file in Gnuplot, otherwise refer to the 
manual section describing the output_format keyword.


You can send GridMAT-MD questions directly to me; there is no need to fill 
peoples' inboxes with non-Gromacs questions.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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Re: [gmx-users] Problem with reading AMBER trajectories

[Mark Abraham]

Can this file be opened in VMD itself?

Mark
On Oct 18, 2013 6:21 AM, "anu chandra"  wrote:

> Dear Gromacs users,
>
> I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing few
> analysis. Unfortunately I ended-up with the following error.
>
> 
> GROMACS will now assume it to be a trajectory and will try to open it using
> the VMD plug-ins.
> This will only work in case the VMD plugins are found and it is a
> trajectory format supported by VMD.
>
> Using VMD plugin: crd (AMBER Coordinates)
>
> Format of file md.crd does not record number of atoms.
>
> ---
> Program g_covar, VERSION 4.6.1
> Source code file: /usr/local/gromacs-4.6.1/src/gmxlib/trxio.c, line: 1035
>
> Fatal error:
> Not supported in read_first_frame: md.crd
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
>
>
>
> While browsing through the GROMACS mail-list, I came to know that it might
> be a problem with DLOPEN libraries. So I recompiled Gromcas with cmake
> using the following command
>
> 
> CMAKE_PREFIX_PATH=/usr/include/libltdl cmake
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs -DCMAKE_C_COMPILER=gcc
> -DCMAKE_CXX_COMPILER=g++ -DFFTWF_LIBRARY=/usr/lib/libfftw3f.a
> -DFFTWF_INCLUDE_DIR=/usr/lib/ ../
> 
>
> But, the same problem came-up again. Can anyone help me to figure out what
> went wrong with my Gromacs installation?
>
> Many thanks in advance.
>
> Regards
> Anu
> --
> 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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