[gmx-users] H-bond analysis
Dear all, I would like to calculate the water residence time for specific protein residues... Therefore I created an index file and used gmx hbonds using the -ac option Every time I have segmentation fault at the beginning of the ac calculation (the calculation of the number of H-bonds is fine). I have also tried to calculate just the number and perform the calculation with gmx analyze using the -luzar option but again I have segmentation fault... Can anyone tell me if I am doing something wrong and how to follow the right procedure? Thanks a lot in avvance. Valerio Ferrario -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx analyze Luzar analysis
Thank you! But still I do not understand what those values represents since there isn´t a legend in the gmx analyze output. I understood that those 3 values should be the average hbond lifetime, and the 2 constant k and k´. Am I correct ? The fitting is bad since I used long simulation time analysis... Reducing the time I obtain the same relaxation values With better integrals: Hydrogen bond thermodynamics at T = 300 K One-way 0.030 33.376 13.321 Integral 0.085 11.729 10.713 Relaxation 1.038 0.963 4.478 Valerio 2017-08-29 14:01 GMT+02:00 Erik Marklund <erik.markl...@kemi.uu.se>: > Dear Valerio, > > Have a glance at the paper by Luzar and Chandler. > > Btw: your data doesn’t fit with the kinetic model very well, hence the > -666 for the integral. > > Kind regards, > Erik > __ > Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow > Department of Chemistry – BMC, Uppsala University > +46 (0)18 471 4539 > erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> > > On 29 Aug 2017, at 13:52, Valerio Ferrario <valerio.ferra...@gmail.com< > mailto:valerio.ferra...@gmail.com>> wrote: > > Dear all, > > I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds > with -ac option but resulted in segmentation fault. Therefore from the > normal gmx hbond output I used gmx analyze to obtain the autocorrelation > function. Therefore, using again gmx analyze with -luzar options and the > autorrelated xvg as input I want to calculate the hbonds parameters. I have > an output like this: > > Hydrogen bond thermodynamics at T = 300 K > One-way 0.006156.395 17.174 > Integral -0.076- 13.220-666.000 > Relaxation 1.0380.963 4.478 > > So my question is: what are the different values? I do not understand what > those values indicate since no "legend" is provide. I guess that 2 of the 3 > values for relaxation might be k and k´ (rate constant for breaking and > reforming hbonds), but I am not sure... Can anyone help me in interpreting > those numbers? > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org<mailto:gmx-users-request@ > gromacs.org>. > > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx analyze Luzar analysis
Dear all, I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds with -ac option but resulted in segmentation fault. Therefore from the normal gmx hbond output I used gmx analyze to obtain the autocorrelation function. Therefore, using again gmx analyze with -luzar options and the autorrelated xvg as input I want to calculate the hbonds parameters. I have an output like this: Hydrogen bond thermodynamics at T = 300 K One-way 0.006156.395 17.174 Integral -0.076- 13.220-666.000 Relaxation 1.0380.963 4.478 So my question is: what are the different values? I do not understand what those values indicate since no "legend" is provide. I guess that 2 of the 3 values for relaxation might be k and k´ (rate constant for breaking and reforming hbonds), but I am not sure... Can anyone help me in interpreting those numbers? -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx spatial
Yes, you are right, but the problem is that if I visualize the trajectory I have the solute around the protein whereas with the spatial distribution function I obtain density function around the protein as well as within the protein core and this make no sense or at least is not convincing. Moreover the trajectory seems very good, with the protein perfectly superposed and with the same orientation in each trajectory step. Is there a way to define the interaction? i.e. the 2 selected groups interacts when they are within a given distance? Best, Valerio 2017-06-28 3:29 GMT+02:00 Dallas Warren <dallas.war...@monash.edu>: > The values for the isosurface are a probability, just like for an RDF, > so negative values don't make any sense. > > Visualise the trajectory you are analysing to see how the solute moves > around, and get a visual idea of if the SDF generated is consistent > with what you are seeing. > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 28 June 2017 at 01:45, Valerio Ferrario <valerio.ferra...@gmail.com> > wrote: > > Dear Users, > > > > I am trying to use the gmx spatial tool in order to understand how a > solute > > interact with the protein. I performed the calculation following all the > > instructions (including the 2 trjconv steps). The trajectory obtained > looks > > fine, and I calculated the sdf with the following command: > > > > gmx_mpi spatial -f CALBtrjvonv2.xtc -s CALBMpr-1.tpr -n X.ndx > > > > and selecting the protein and an atom of my solute molecules (in the > index) > > > > but when I open the grid.cube file with vmd and I visualize it as > > isosurface I have the density function even within the protein core... I > > thought that the density should be just around the protein (in this > case). > > Moreover I have just positive values for the isosurface, is that normal? > Am > > I doing something wrong? > > > > Thanks a lot, > > Valerio Ferrario > > -- > > 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 > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx spatial
Dear Users, I am trying to use the gmx spatial tool in order to understand how a solute interact with the protein. I performed the calculation following all the instructions (including the 2 trjconv steps). The trajectory obtained looks fine, and I calculated the sdf with the following command: gmx_mpi spatial -f CALBtrjvonv2.xtc -s CALBMpr-1.tpr -n X.ndx and selecting the protein and an atom of my solute molecules (in the index) but when I open the grid.cube file with vmd and I visualize it as isosurface I have the density function even within the protein core... I thought that the density should be just around the protein (in this case). Moreover I have just positive values for the isosurface, is that normal? Am I doing something wrong? Thanks a lot, Valerio Ferrario -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
