RE: [gmx-users] Conversion of nm to Å
First port of call for a question like this should be a search engine http://en.wikipedia.org/wiki/Angstrom Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Arunima Shilpi > Sent: Wednesday, 21 August 2013 1:06 PM > To: gmx-users@gromacs.org > Subject: [gmx-users] Conversion of nm to Å > > Dear Sir > I have to query as to how do we convert the paramaters in "nm" to Å > --. For example the RMSD and RMSF calculation gives result in "nm". I > want > to convert > it to Å. I request you to kindly guide me with the process > > Thanking You with Regards. > > Arunima Shilpi > > Ph. D Research Scholar(Cancer & Epigenetics) > Department of Life Science > National Institute of Technology > Rourkela > Odisha > -- > 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 -- 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
[gmx-users] Conversion of nm to Å
Dear Sir I have to query as to how do we convert the paramaters in "nm" to Å --. For example the RMSD and RMSF calculation gives result in "nm". I want to convert it to Å. I request you to kindly guide me with the process Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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
Re: [gmx-users] Number of SOL/Water in gmx_moltype_t
What about OHN - the hydroxyl radical? I put two of them in the system to
understand the issue. Under DNA_chain_X, you clearly see nr=2 for OHN. If I
take one OHN out from pdb (means one DTMP, one OHN and water), I again get
nr=1 for OHN.
residue (2):
> residue[0]={name="DTMP", nr=1, ic=' '}
> residue[1]={name="OHN", nr=2, ic=' '}
Pradip
On Tue, Aug 20, 2013 at 3:12 PM, Mark Abraham wrote:
> residue is a sub-field of moltype, so you are seeing that there is
> indeed one SOL residue per water molecule, as expected. Look elsewhere
> and you will see that there are 351 of those molecules recorded. The
> same is true of the DNA chain, but since there's only one DNA chain,
> the number of residues per molecule coincides with the number in the
> system.
>
> Mark
>
> On Tue, Aug 20, 2013 at 7:48 PM, Pradip Biswas
> wrote:
> > Hi,
> >
> > I am using v-4.5.5. I have a system of DNA nucleotide & *two* OH radicals
> > solvated in water.
> >
> > The topology file has the following records in the end:
> >
> > [ molecules ]
> > ; Compound#mols
> > DNA_chain_X 1
> > SOL351
> >
> >
> > However, when I did gmxdump after running grompp, I see the following:
> >
> > moltype (0):
> > name="DNA_chain_X"
> > ...
> > ...
> > residue (2):
> > residue[0]={name="DTMP", nr=1, ic=' '}
> > residue[1]={name="OHN", nr=2, ic=' '}
> >
> >
> > moltype (1):
> > name="SOL"
> > ..
> > ..
> > residue (1):
> > residue[0]={name="SOL", *nr=1*, ic=' '}
> >
> > Aren't we recording the number of solvent residues? I was expecting
> nr=351
> > for SOL; the number of water molecule I have in the system. As I get nr=2
> > for OHN
> >
> > Thanks,
> > Pradip Biswas
> >
> >
> >
> > --
> > P. K. Biswas, PhD
> > Laboratory of Computational Biophysics & Bioengineering
> > Associate Professor of Physics
> > Tougaloo College
> > 601-977-7788
> > --
> > 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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> > www interface or send it to gmx-users-requ...@gromacs.org.
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> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
--
P. K. Biswas, PhD
Laboratory of Computational Biophysics & Bioengineering
Associate Professor of Physics
Tougaloo College
601-977-7788
--
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RE: [gmx-users] Coordination number
Peak can be higher, but if it is narrower the total area can still be less. Remember it is an area under the curve. Additionally, that overall system / box density that you are using may be different too, so that will make a difference. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Venkat Reddy > Sent: Monday, 19 August 2013 8:11 PM > To: Discussion list for GROMACS users > Subject: [gmx-users] Coordination number > > Dear Gromacs Users, > > I have a query about the g_rdf utility. I have two different systems of > water with Ionic Liquid 1 and Ionic Liquid 2. When I plot the rdf using > > g_rdf -f x_gro.pdb -s x.pdb -n rdf.ndx -o rdf1.xvg/rdf2.xvg -cn > rdf1_cn.xvg/rdf2_cn.xvg -rdf res_com > > where rdf1/rdf2 is for water distribution around Ionic liquid 1/2, > > the rdf1.xvg clearly shows a higher first peak g(r) than the rdf2.xvg. > Both > also have minima at the same distance. However, the coordination number > at > first minima from rdf1_cn.xvg is lesser than the same from rd2_cn.xvg. > How > is this possible? If the peak is larger, the integration of it should > give > a higher value right? > > Please help. > > > -- > With Best Wishes > Venkat Reddy Chirasani > PhD student > Laboratory of Computational Biophysics > Department of Biotechnology > IIT Madras > Chennai > INDIA-600036 > -- > 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 -- 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
Re: [gmx-users] Number of SOL/Water in gmx_moltype_t
residue is a sub-field of moltype, so you are seeing that there is
indeed one SOL residue per water molecule, as expected. Look elsewhere
and you will see that there are 351 of those molecules recorded. The
same is true of the DNA chain, but since there's only one DNA chain,
the number of residues per molecule coincides with the number in the
system.
Mark
On Tue, Aug 20, 2013 at 7:48 PM, Pradip Biswas wrote:
> Hi,
>
> I am using v-4.5.5. I have a system of DNA nucleotide & *two* OH radicals
> solvated in water.
>
> The topology file has the following records in the end:
>
> [ molecules ]
> ; Compound#mols
> DNA_chain_X 1
> SOL351
>
>
> However, when I did gmxdump after running grompp, I see the following:
>
> moltype (0):
> name="DNA_chain_X"
> ...
> ...
> residue (2):
> residue[0]={name="DTMP", nr=1, ic=' '}
> residue[1]={name="OHN", nr=2, ic=' '}
>
>
> moltype (1):
> name="SOL"
> ..
> ..
> residue (1):
> residue[0]={name="SOL", *nr=1*, ic=' '}
>
> Aren't we recording the number of solvent residues? I was expecting nr=351
> for SOL; the number of water molecule I have in the system. As I get nr=2
> for OHN
>
> Thanks,
> Pradip Biswas
>
>
>
> --
> P. K. Biswas, PhD
> Laboratory of Computational Biophysics & Bioengineering
> Associate Professor of Physics
> Tougaloo College
> 601-977-7788
> --
> 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.
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--
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[gmx-users] Number of SOL/Water in gmx_moltype_t
Hi,
I am using v-4.5.5. I have a system of DNA nucleotide & *two* OH radicals
solvated in water.
The topology file has the following records in the end:
[ molecules ]
; Compound#mols
DNA_chain_X 1
SOL351
However, when I did gmxdump after running grompp, I see the following:
moltype (0):
name="DNA_chain_X"
...
...
residue (2):
residue[0]={name="DTMP", nr=1, ic=' '}
residue[1]={name="OHN", nr=2, ic=' '}
moltype (1):
name="SOL"
..
..
residue (1):
residue[0]={name="SOL", *nr=1*, ic=' '}
Aren't we recording the number of solvent residues? I was expecting nr=351
for SOL; the number of water molecule I have in the system. As I get nr=2
for OHN
Thanks,
Pradip Biswas
--
P. K. Biswas, PhD
Laboratory of Computational Biophysics & Bioengineering
Associate Professor of Physics
Tougaloo College
601-977-7788
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference
Hi, Rajat- We are working on ways to make the workshop materials available online, either streaming or posted afterwards. The tutorials will have online components as well. We were unable to obtain travel funding for the conference this year, unfortunately! > I would be willing to pay the whole workshop fee (and more) if you could > kindly video the whole workshop and make it available to us. Thank you. We are not planning on charging for the material, but we should make it easier to donate if you wanted to after we get this material out! On Tue, Aug 20, 2013 at 12:14 AM, rajat desikan wrote: > Hi Prof. Shirts, > I am sure that I speak for a lot of GROMACS users when I say that I want to > attend the workshop, but I cannot. I would be willing to pay the whole > workshop fee (and more) if you could kindly video the whole workshop and > make it available to us. Thank you. > > > On Tue, Aug 20, 2013 at 10:50 AM, Michael Shirts < > michael.shi...@virginia.edu> wrote: > >> Dear GROMACS users- >> >> I'd like to remind you all about the 2013 GROMACS USA Workshop and >> Conference at the University of Virginia Sept 13th-15th. There are >> still registration slots available, but the early registration >> deadline of Aug 22nd is coming up in just a few days; after the 22nd, >> the registration price will rise from the very low $60 for the two day >> conference to the moderately-low-but-why-pay-more $95. >> >> As mentioned in previous emails to the list, the workshop and >> conference will consist of two days of tutorials, discussions of >> future plans for GROMACS, face time with many of the main GROMACS >> developers, plenary software and application sessions, and an optional >> last day of development planning to which attendees are also invited >> to help influence the future directions of GROMACS. >> >> Please visit http://faculty.virginia.edu/gromacsworkshop for >> registration and for much more information about the workshop, >> including travel logistics. The website was also recently has been >> updated with more specifics about the program. >> >> For specific questions about registering or logistics after visiting >> the website, please write to >> gromacsworkshop-registrat...@virginia.edu. >> >> Sincerely, >> The 2013 GROMACS USA Workshop and Conference Steering Committee >> Michael Shirts (chair) >> Angel Garcia >> Berk Hess >> Yu-Shan Lin >> Erik Lindahl >> Peter Kasson >> -- >> 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 >> > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- > 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 -- 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
Re: [gmx-users] g_WHAM
On 8/20/13 9:59 AM, Shima Arasteh wrote: Hi, I have a tpr-files.dat containing 5 tpr files as it: 4.tpr 5.tpr 6.tpr 7.tpr 8.tpr Also the pullf-files.dat is in accordance with tpr-files.dat. But when I run g_wham and visualize the histo output, I see only one curve and not 4 curves which are expected to have appropriate overlaps! Would you please let me know how come? Is it usual to get one curve from each histo.xvg? You're probably plotting histo.xvg wrong. xmgrace -nxy histo.xvg When in doubt, just open it in a text editor to confirm its contents. -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 == -- 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
[gmx-users] g_WHAM
Hi, I have a tpr-files.dat containing 5 tpr files as it: 4.tpr 5.tpr 6.tpr 7.tpr 8.tpr Also the pullf-files.dat is in accordance with tpr-files.dat. But when I run g_wham and visualize the histo output, I see only one curve and not 4 curves which are expected to have appropriate overlaps! Would you please let me know how come? Is it usual to get one curve from each histo.xvg? Thanks for your suggestions. I appreciate you in advance. Sincerely, Shima From: Justin Lemkul To: Discussion list for GROMACS users Sent: Thursday, August 8, 2013 11:08 PM Subject: Re: [gmx-users] g_WHAM On 8/8/13 2:37 PM, Shima Arasteh wrote: > g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCalvv > > It's the error what get; > File input/output error: > tpr-files.dat > Then a file named "tpr-files.dat" does not exist in the working directory. Check for typos and the existence of the file. -Justin > > > Sincerely, > Shima > > > - Original Message - > From: Justin Lemkul > To: Shima Arasteh ; Discussion list for GROMACS > users > Cc: > Sent: Thursday, August 8, 2013 10:45 PM > Subject: Re: [gmx-users] g_WHAM > > > > On 8/8/13 2:13 PM, Shima Arasteh wrote: >> Hi, >> >> Would you please let me know if it is possible to get just the first 2 >> histograms of total 24 histograms by running g_WHAM? >> I mean the tpr-files.dat contains only 2 .tpr files of umbrella sampling >> simulations and not the all. >> >> I ran such dat file, but doesn't work and gives me an error of no input file. > > The exact error, copied and pasted from the terminal, is more useful. > >> g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal >> > > As long as pullf-files.dat and tpr-files.dat both specify the same number of > input files and the .tpr and .xvg files therein match, there should be no > problem. > > -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 == -- 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! * 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 -- 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
Re: [gmx-users] Re: GPU version of Gromacs
On 8/20/13 5:52 AM, grita wrote: Dear Dwey & Justin, I've not tried it yet and I've asked because in the 4.5.x GPU version of Gromacs not all features were supported. In my simulations I'm using the SD integrator and the Pull-Code. Since both are supported in the current GPU version, I will try it on a computer with a CUDA graphic card. Versions in the 4.5.x series only support GPU acceleration via OpenMM and thus most Gromacs features are not supported. Native GPU support in 4.6 is much more comprehensive. -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 == -- 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
[gmx-users] Re: GPU version of Gromacs
Dear Dwey & Justin, I've not tried it yet and I've asked because in the 4.5.x GPU version of Gromacs not all features were supported. In my simulations I'm using the SD integrator and the Pull-Code. Since both are supported in the current GPU version, I will try it on a computer with a CUDA graphic card. Many thanks, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/GPU-version-of-Gromacs-tp5010581p5010627.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
