[gmx-users] Re: Covariance file format
Hi Tsjerk, Coffee is always magical, I tell you. Just a sniff in the air and it makes things clear. So, 1/n sum is the mass weighted ness? And x1 to zn spans from 1 to 1992? By any chance we don't obtain a file I. Which the first column wud have alpha atom one second column would have 2nd aloha atom n third would have correlation between them? Kind regards, Ankita On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > Hi Ankita, > > I should not answer questions before coffee!! Sorry. > > It's the covariance matrix! So it's > > 1/n sum x1x1 1/n sum x1y1 1/n sum x1z1 > 1/n sum x1x2 1/n sum x1y2 1/n sum x1z2 > ... > 1/n sum zNxN 1/n sum zNyN 1/n sum zNzN > > Silly me :| > > Tsjerk > > > On Mon, Jul 1, 2013 at 8:09 AM, Ankita naithani > > >wrote: > > > Hi Tsjerk, > > Thank you for your reply. So, these are the eigenvectors. By any chance, > > can we obtain the covariance matrix containing the information of residue > > fluctuations I.e. the covariance information. Actually, it was needed to > > obtain the dot plot delta ri dot delta rj so I don't think so I can use > the > > eigenvectors > > > > > > Kind regards > > > > Ankita > > > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > > > Hi Ankita, > > > > > > The fie contains the eigenvectors as > > > > > > x1 y1 z1 > > > x2 y2 z2 > > > ... > > > xN yN zN > > > > > > Hope it helps, > > > > > > Tsjerk > > > > > > > > > On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani < > > ankitanaith...@gmail.com > > > >wrote: > > > > > > > Hi, > > > > > > > > I wanted to know the exact format of covariance.dat file as generated > > by > > > > g_covar during covariance analysis. The file format mentioned in the > > > manual > > > > was not quite clear to understand. I need to use the matrix > > information n > > > > so needed to know how the data is stored. My matrix is for 1992 > calpha > > > > atoms. > > > > > > > > It would be really helpful if someone could explain the file format. > > > > > > > > Kind regards, > > > > > > > > Ankita > > > > > > > > > > > > -- > > > > Ankita Naithani > > > > -- > > > > 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 > > > > > > > > > > > > > > > > -- > > > 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! > > > * 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 > > > > > > > > > -- > > Ankita Naithani > > -- > > 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 > > > > > > -- > 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! > * 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 > -- Ankita Naithani -- 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] Angle Distribution
Dear All, Do you know how can I calculate angular distribution of all angles in my system? Shall I specify in one index group all e.g. 80 atoms so g_angle will calculate all possibile distributions and plot it as a sum? Steven -- 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: Angle Distribution
The other issue... I am using tables as an input in my protein coarse grained model based on atomistic simulations. I used Boltzmann inversion and fitted the curve into the 6th order polynomial then in angle_a*.xvg I used -f ' (x) so the derivative of my polynomial. My question: Do I need to use it as a function which will describe the angular potential? Can I just refine and smooth it? But how I am going to calculate the derivative? Steven On Mon, Jul 1, 2013 at 8:19 AM, Steven Neumann wrote: > Dear All, > > Do you know how can I calculate angular distribution of all angles in my > system? Shall I specify in one index group all e.g. 80 atoms so g_angle > will calculate all possibile distributions and plot it as a sum? > > Steven > -- 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] ANN: mdtraj 0.3 released
I am pleased to announce the release of mdtraj 0.3. Description mdtraj is a library for loading, saving, and manipulating molecular dynamics trajectories in the python programming language. It supports the RCSB PDB, Gromacs XTC and TRR, CHARMM / NAMD DCD, AMBER binpos, AMBER NetCDF and MDTraj HDF5 formats. It based on numpy and cython, and licensed under the the GPL. home page: http://rmcgibbo.github.io/mdtraj/ code (github): https://github.com/rmcgibbo/mdtraj installation: pip install mdtraj Highlights -- - Cross-format trajectory file support, including memory efficient subsampled load operations. - Fast RMSD calculations via Imran Haque's IRMSD library. This SSE2/3-based RMSD code computes protein optimal root-mean-square deviations using the quaternion characteristic polynomial (Theobald QCP) method at 4x the speed of the original Theobald code. - mdconvert: a command-line script for converting trajectory files between all pairs of supported formats. Enjoy! -Robert -- 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] D-aminoacids in input file
Dear gmx users, I have D amino acids in my input .pdb file. The force field which I aim to use, is CHARMM. I am wondering if I need to modify aminoacids.rtp file? Or it would be OK if I use the same parameters as L aminoacids for D aminoacids? Thanks for your suggestions. They would be appreciated. Sincerely, Shima -- 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: Covariance file format
Hi Ankita, No, the file contains the 3Nx3N covariance matrix, row by row, split over triplets, mass weighted if you did the analysis mass-weighted. But for C-alpha only there is no difference between mass-weighted and non-mass-weighted, except for global scaling. Cheers, Tsjerk On Mon, Jul 1, 2013 at 8:46 AM, Ankita naithani wrote: > Hi Tsjerk, > > Coffee is always magical, I tell you. Just a sniff in the air and it makes > things clear. > > So, 1/n sum is the mass weighted ness? And x1 to zn spans from 1 to 1992? > > By any chance we don't obtain a file I. Which the first column wud have > alpha atom one second column would have 2nd aloha atom n third would have > correlation between them? > > > > Kind regards, > > Ankita > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > Hi Ankita, > > > > I should not answer questions before coffee!! Sorry. > > > > It's the covariance matrix! So it's > > > > 1/n sum x1x1 1/n sum x1y1 1/n sum x1z1 > > 1/n sum x1x2 1/n sum x1y2 1/n sum x1z2 > > ... > > 1/n sum zNxN 1/n sum zNyN 1/n sum zNzN > > > > Silly me :| > > > > Tsjerk > > > > > > On Mon, Jul 1, 2013 at 8:09 AM, Ankita naithani < > ankitanaith...@gmail.com > > >wrote: > > > > > Hi Tsjerk, > > > Thank you for your reply. So, these are the eigenvectors. By any > chance, > > > can we obtain the covariance matrix containing the information of > residue > > > fluctuations I.e. the covariance information. Actually, it was needed > to > > > obtain the dot plot delta ri dot delta rj so I don't think so I can use > > the > > > eigenvectors > > > > > > > > > Kind regards > > > > > > Ankita > > > > > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > > > > > Hi Ankita, > > > > > > > > The fie contains the eigenvectors as > > > > > > > > x1 y1 z1 > > > > x2 y2 z2 > > > > ... > > > > xN yN zN > > > > > > > > Hope it helps, > > > > > > > > Tsjerk > > > > > > > > > > > > On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani < > > > ankitanaith...@gmail.com > > > > >wrote: > > > > > > > > > Hi, > > > > > > > > > > I wanted to know the exact format of covariance.dat file as > generated > > > by > > > > > g_covar during covariance analysis. The file format mentioned in > the > > > > manual > > > > > was not quite clear to understand. I need to use the matrix > > > information n > > > > > so needed to know how the data is stored. My matrix is for 1992 > > calpha > > > > > atoms. > > > > > > > > > > It would be really helpful if someone could explain the file > format. > > > > > > > > > > Kind regards, > > > > > > > > > > Ankita > > > > > > > > > > > > > > > -- > > > > > Ankita Naithani > > > > > -- > > > > > 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 > > > > > > > > > > > > > > > > > > > > > -- > > > > Tsjerk A. Wassenaar, Ph.D. > > > > -- > > > > 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 > > > > > > > > > > > > > -- > > > Ankita Naithani > > > -- > > > 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 > > > > > > > > > > > -- > > 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! > > * 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 > > > > > -- > Ankita Naithani > -- > 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
[gmx-users] Re: Covariance file format
Hi Tsjerk, Thank you very much. It was extremely helpful. Kind regards Ankita On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > Hi Ankita, > > No, the file contains the 3Nx3N covariance matrix, row by row, split over > triplets, mass weighted if you did the analysis mass-weighted. But for > C-alpha only there is no difference between mass-weighted and > non-mass-weighted, except for global scaling. > > Cheers, > > Tsjerk > > > > On Mon, Jul 1, 2013 at 8:46 AM, Ankita naithani > > >wrote: > > > Hi Tsjerk, > > > > Coffee is always magical, I tell you. Just a sniff in the air and it > makes > > things clear. > > > > So, 1/n sum is the mass weighted ness? And x1 to zn spans from 1 to 1992? > > > > By any chance we don't obtain a file I. Which the first column wud have > > alpha atom one second column would have 2nd aloha atom n third would have > > correlation between them? > > > > > > > > Kind regards, > > > > Ankita > > > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > > > Hi Ankita, > > > > > > I should not answer questions before coffee!! Sorry. > > > > > > It's the covariance matrix! So it's > > > > > > 1/n sum x1x1 1/n sum x1y1 1/n sum x1z1 > > > 1/n sum x1x2 1/n sum x1y2 1/n sum x1z2 > > > ... > > > 1/n sum zNxN 1/n sum zNyN 1/n sum zNzN > > > > > > Silly me :| > > > > > > Tsjerk > > > > > > > > > On Mon, Jul 1, 2013 at 8:09 AM, Ankita naithani < > > ankitanaith...@gmail.com > > > >wrote: > > > > > > > Hi Tsjerk, > > > > Thank you for your reply. So, these are the eigenvectors. By any > > chance, > > > > can we obtain the covariance matrix containing the information of > > residue > > > > fluctuations I.e. the covariance information. Actually, it was needed > > to > > > > obtain the dot plot delta ri dot delta rj so I don't think so I can > use > > > the > > > > eigenvectors > > > > > > > > > > > > Kind regards > > > > > > > > Ankita > > > > > > > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > > > > > > > Hi Ankita, > > > > > > > > > > The fie contains the eigenvectors as > > > > > > > > > > x1 y1 z1 > > > > > x2 y2 z2 > > > > > ... > > > > > xN yN zN > > > > > > > > > > Hope it helps, > > > > > > > > > > Tsjerk > > > > > > > > > > > > > > > On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani < > > > > ankitanaith...@gmail.com > > > > > >wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > I wanted to know the exact format of covariance.dat file as > > generated > > > > by > > > > > > g_covar during covariance analysis. The file format mentioned in > > the > > > > > manual > > > > > > was not quite clear to understand. I need to use the matrix > > > > information n > > > > > > so needed to know how the data is stored. My matrix is for 1992 > > > calpha > > > > > > atoms. > > > > > > > > > > > > It would be really helpful if someone could explain the file > > format. > > > > > > > > > > > > Kind regards, > > > > > > > > > > > > Ankita > > > > > > > > > > > > > > > > > > -- > > > > > > Ankita Naithani > > > > > > -- > > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > 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! > > > > > * 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 > > > > > > > > > > > > > > > > > -- > > > > Ankita Naithani > > > > -- > > > > 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 > > > > > > > > > > > > > > > > -- > > > 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! > > > * Please don't post (un)subscribe r
Re: [gmx-users] D-aminoacids in input file
Hi Shima, You can use the same parameters. There is no difference other than the position of atoms. Cheers, Tsjerk On Mon, Jul 1, 2013 at 9:52 AM, Shima Arasteh wrote: > Dear gmx users, > > I have D amino acids in my input .pdb file. The force field which I aim to > use, is CHARMM. I am wondering if I need to modify aminoacids.rtp file? Or > it would be OK if I use the same parameters as L aminoacids for D > aminoacids? > > > > Thanks for your suggestions. They would be appreciated. > > Sincerely, > Shima > -- > 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 > -- 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! * 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] TPI Results differ in v4.5.7 and v4.6.1
I have run TPI using three versions (4.0.4, 4.5.4 and 4.6.1) and three different insertions particles: CH4 (uncharged), Cl- (negative) and Na+ (positive). All TPI were run on the same simulations of SPC water and the three particles taken from GROMOS force-field. Reaction-field was used for electrostatics. https://www.dropbox.com/s/in66zx8t2mrprgt/plot_batch-1.png As you can see, for an uncharged particle all the versions provide the same result. The same does not happen when charged particles are inserted, which hint on problems with the electrostatics between 4.0.4 and 4.[56].X. Like when Niels reported for the Cut-off scheme, the reaction-field provides the same results for 4.5.4 and 4.6.1. Is it indeed a problem with PME? I still have not tested PME, but I think Niels' test foretells the results I'm going to get. Niels, can you confirm this issue is only happening with charged particles? And are you going to file an issue like Szilárd suggested? Best, João On Sat, Jun 29, 2013 at 5:21 PM, João M. Damas wrote: > Niels, > > Which force-field did you use? I guess an uncharged CH4 shouldn't be > giving different results for TPI when changing coulomb... Actually, coulomb > is turned off if there's no charge in the particles to insert, if I > remember the code correctly. > > João > > > On Mon, Jun 24, 2013 at 3:40 PM, Niels Müller wrote: > >> Hi João, >> >> Indeed your instinct seems to be good! When switching the Coulomb-Type to >> Cut-Off, there doesn't seem to be a difference between 4.6 and 4.5. >> Apparently its an issue with the PME sum. We will investigate further. >> >> >> Am 24.06.2013 um 14:42 schrieb João M. Damas : >> >> > Niels, >> > >> > This is very interesting. At our group, a colleague of mine and I have >> also >> > identified differences in the TPI integrator between 4.0.X and 4.5.X, >> but >> > we still haven't had the time to report it properly, since we are using >> a >> > slightly modified version of the TPI algorithm. >> > >> > Instinctively, we were attributing it to some different behaviours in >> the >> > RF that are observed between those versions. We also know that the TPI >> > algorithm began allowing PME treatment from 4.5.X onwards, so maybe >> there >> > are some differences going on the electrostatics level? But, IIRC, no >> > modifications to the TPI code were on the release notes from 4.5.X to >> > 4.6.X... >> > >> > We'll try to find some time to report our findings as soon as possible. >> > Maybe they are related. >> > >> > Best, >> > João >> > >> > >> > On Mon, Jun 24, 2013 at 10:19 AM, Niels Müller wrote: >> > >> >> Hi GMX Users, >> >> >> >> We are computing the chemical potential of different gas molecules in a >> >> polymer melt with the tpi integrator. >> >> The computations are done for CO2 and CH4. >> >> The previous computations were done with v4.5.5 or 4.5.7 and gave equal >> >> results. >> >> >> >> I recently switched to gromacs version 4.6.1, and the chemical >> potential >> >> computed by this version is shifted by a nearly constant factor, which >> is >> >> different for the two gas molecules. >> >> We are perplexed what causes this shift. Was there any change in the >> new >> >> version that affects the tpi integration? I will provide the mdp file >> we >> >> used below. >> >> >> >> The tpi integration is run on basis of the last 10 ns of a 30 ns NVT >> >> simulation with 'mdrun -rerun'. >> >> >> >> Best regards, >> >> Niels. >> >> >> >> # >> >> The mdp file: >> >> # >> >> >> >> ; VARIOUS PREPROCESSING OPTIONS >> >> cpp = cpp >> >> include= >> >> define = >> >> >> >> ; RUN CONTROL PARAMETERS >> >> integrator = tpi >> >> ; Start time and timestep in ps >> >> tinit= 0 >> >> dt = 0.001 >> >> nsteps = 100 >> >> ; For exact run continuation or redoing part of a run >> >> init_step= 0 >> >> ; mode for center of mass motion removal >> >> comm-mode= Linear >> >> >> >> ; number of steps for center of mass motion removal >> >> nstcomm = 1 >> >> ; group(s) for center of mass motion removal >> >> comm-grps= >> >> >> >> ; LANGEVIN DYNAMICS OPTIONS >> >> ; Temperature, friction coefficient (amu/ps) and random seed >> >> bd-fric = 0.5 >> >> ld-seed = 1993 >> >> >> >> ; ENERGY MINIMIZATION OPTIONS >> >> ; Force tolerance and initial step-size >> >> emtol= 100 >> >> emstep = 0.01 >> >> ; Max number of iterations in relax_shells >> >> niter= 20 >> >> ; Step size (1/ps^2) for minimization of flexible constraints >> >> fcstep = 0 >> >> ; Frequency of steepest descents steps when doing CG >> >> nstcgsteep = 1000 >> >> nbfgscorr= 10 >> >> >> >> ; OUTPUT CONTROL OPTIONS >> >> ; Output fre
[gmx-users] Computational slow downs when using oscillatory electric field
Hello, I am using the oscillatory electric field function in gromacs 4.6.1. I have experienced slow downs in computation efficiency (50% decrease or more) between the oscillatory electric field simulations and simulations with no applied electric field. Has anyone experience similar decreases in efficiency? Has anyone overcome these problems? I am simulating a large system (e.g. millions of atoms including explicit water) and that could be part of the problem, but I still experience large slow downs going from no applied field to applied oscillatory field. Any insights are appreciated. Thanks so much, Ross Quick -- 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] Computational slow downs when using oscillatory electric field
I would expect the applied-field code got no work during the lead-up to 4.6, but I can see no obvious reason why it should run slowly. Please use diff on your .log files and gmxcheck on your .tpr files to see what can be learned about what is actually different. Mark On Mon, Jul 1, 2013 at 6:44 PM, Quick, Ross wrote: > Hello, > > I am using the oscillatory electric field function in gromacs 4.6.1. I have > experienced slow downs in computation efficiency (50% decrease or more) > between the oscillatory electric field simulations and simulations with no > applied electric field. Has anyone experience similar decreases in > efficiency? Has anyone overcome these problems? I am simulating a large > system (e.g. millions of atoms including explicit water) and that could be > part of the problem, but I still experience large slow downs going from no > applied field to applied oscillatory field. > > Any insights are appreciated. Thanks so much, > > Ross Quick > -- > 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] energy groups for specific parts of the molecule
Dear Gromacs users, I ran a simulation between 6 molecules of Hypericin and 26 base pair long DNA, so for energy_grps I set HYP and DNA. Is there any way to get van der Waals and coulomb energy's of the interaction between hypericin and a specific parts of the DNA(phosphate groups for example)? Are there any tutorials? Thanks in advance, Hovakim Grabski Russia- Armenian(Slavonic) University -- 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] energy groups for specific parts of the molecule
On 7/1/13 7:00 PM, Hovakim Grabski wrote: Dear Gromacs users, I ran a simulation between 6 molecules of Hypericin and 26 base pair long DNA, so for energy_grps I set HYP and DNA. Is there any way to get van der Waals and coulomb energy's of the interaction between hypericin and a specific parts of the DNA(phosphate groups for example)? Are there any tutorials? Just make each molecule its own group and set those as your energygrps. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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] TRACE OF RMSD COMPARISON MATRIX
Hello users, I'm using g_rms to compare my actual trajectory obtained from simulation with the filtered trajectory (along given set of eigenvectors), this gives me an RMSD comparison matrix in xpm format where the values of the plot are not clear. Is there any way which can help me to get the values along the diagonal of the matrix? the command that i followed is: g_rms -s ref.tpr -f actual.xtc -f2 filtered.xtc -m rmsd.xpm I want to calculate the trace of the matrix basically. Regards.. -- 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] TRACE OF RMSD COMPARISON MATRIX
Following link might be helpful: http://orbeckst.github.io/GromacsWrapper/gromacs/core/fileformats/xpm.html -g -- Gaurav Goel Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India On 02-Jul-2013, at 10:45 AM, Richa Singh wrote: > Hello users, > > I'm using g_rms to compare my actual trajectory obtained from > simulation with the filtered trajectory (along given set of > eigenvectors), this gives me an RMSD comparison matrix in xpm format > where the values of the plot are not clear. Is there any way which can > help me to get the values along the diagonal of the matrix? > the command that i followed is: > g_rms -s ref.tpr -f actual.xtc -f2 filtered.xtc -m rmsd.xpm > > I want to calculate the trace of the matrix basically. > > > Regards.. > -- > 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
