Re: [gmx-users] trjcat skipping frames
The old information is given below. I haven't chopped into the code yet to see if Berk's fix is there. http://www.mail-archive.com/gmx-users@gromacs.org/msg14689.html ~j Quoting "Justin A. Lemkul" : > > > Jared James Thompson wrote: > > Hi All, > > > > I'm having a problem with trjcat skipping frames. I saw a similar > complaint > > seemingly handled by Berk Hess in 2008. I wanted to know if his bug fix has > been > > incorporated into the current gromacs version. > > > > Can you provide a link to this information? What version of Gromacs are you > > using? Presumably, if you're using the latest version, bugs from 2 years ago > > should be fixed. > > > I have a number of short .trj files of equal length and time spacing that I > want > > to cat together to form a single .trj file. I have a method for doing this > using > > trjcat and trjconv. It has worked normally in the past. > > > > The method is as follows. Set the start time of each trajectory to be the > next > > putative frame immediately following the previous trajectory, and also set > the > > timestep for each frame correctly, so for .trj of 10 frames long: > > > > trjconv -f frame_traj_2.trr -o ftc_2.trr -t0 20 -timestep 1.0 > > > > trjconv -f frame_traj_3.trr -o ftc_3.trr -t0 30 -timestep 1.0 > > > > etc. > > > > Once all the frame_traj_x files are together, then use trjcat to cat them. > > > > trjcat -f ftc* -o CombinedTraj.trj > > > > > > However, this time that I am using it, trjcat is producing the following > > response, note the timestep shown in the File Roster and that ftc_5 is > treated > > normally for some reason: > > > > FileStart time Time step > > - > > ftc_1.trr0.000 ps1.000 ps > > ftc_2.trr 20.000 ps0.000 ps > > ftc_3.trr 40.000 ps0.000 ps > > Clearly something has broken down on a very fundamental level. You set > ftc_3.trr to have a start time of 30 ps above, but it has not worked. > > Some questions that may help diagnose your issue: > > 1. What is the spacing of frames in your original .trr files? > 2. What does gmxcheck tell you about each of your ftc_*.trr files? > 3. Does passing -t0 and -timestep to trjconv in separate steps make any > difference? > > -Justin > > -- > ==== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] trjcat skipping frames
Hi All, I'm having a problem with trjcat skipping frames. I saw a similar complaint seemingly handled by Berk Hess in 2008. I wanted to know if his bug fix has been incorporated into the current gromacs version. I have a number of short .trj files of equal length and time spacing that I want to cat together to form a single .trj file. I have a method for doing this using trjcat and trjconv. It has worked normally in the past. The method is as follows. Set the start time of each trajectory to be the next putative frame immediately following the previous trajectory, and also set the timestep for each frame correctly, so for .trj of 10 frames long: trjconv -f frame_traj_2.trr -o ftc_2.trr -t0 20 -timestep 1.0 trjconv -f frame_traj_3.trr -o ftc_3.trr -t0 30 -timestep 1.0 etc. Once all the frame_traj_x files are together, then use trjcat to cat them. trjcat -f ftc* -o CombinedTraj.trj However, this time that I am using it, trjcat is producing the following response, note the timestep shown in the File Roster and that ftc_5 is treated normally for some reason: FileStart time Time step - ftc_1.trr0.000 ps1.000 ps ftc_2.trr 20.000 ps0.000 ps ftc_3.trr 40.000 ps0.000 ps ftc_4.trr 60.000 ps0.000 ps ftc_5.trr 80.000 ps1.000 ps Back Off! I just backed up CombinedTraj.trr to ./#CombinedTraj.trr.3# Reading frame 0 time0.000 Continue writing frames from ftc_1.trr t=0 ps, frame=0 Last frame 20 time 20.000-> frame 10 time 10.000 ps Reading frame 0 time 20.000 lasttime 19 Continue writing frames from ftc_2.trr t=20 ps, frame=20 Last frame 0 time 20.000 WARNING: Frames around t=20.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 40.000 lasttime 20 Continue writing frames from ftc_3.trr t=40 ps, frame=21 Last frame 0 time 40.000 WARNING: Frames around t=40.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 60.000 lasttime 40 Continue writing frames from ftc_4.trr t=60 ps, frame=22 Last frame 0 time 60.000 WARNING: Frames around t=60.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 80.000 lasttime 60 Continue writing frames from ftc_5.trr t=80 ps, frame=23 Last frame 20 time 100.000-> frame 40 time 97.000 ps Last frame written was 43, time 100.00 ps Any help would be appreciated. Best, Jared Thompson -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] coarse grain dynamics
I agree with Justin on this one. Simulations run using CG that is not optimized for reconstruction may not actually reflect the type of interactions you are looking for. The current result of this simulation may not directly correspond to a full atomistic result, so even if a reconstruction were performed you would most likely NOT be able to draw conclusions from it. Otherwise, everyone would run really fast simulations in CG, then reconstruct their systems afterward. :) Quoting "Justin A. Lemkul" : > > > ram bio wrote: > > thanks, > > > > but i am using gromacs version 4.0.07 > > > > I think the general consensus thus far is you won't be able to do what you > want > without significant effort to reconstruct your system, and perhaps then you > should question whether any tools that seek to build optimal hydrogens from > CG > structures are going to bias the result. Would those hydrogen bonds have > actually formed in an AA simulation? Hard to tell. If you want to analyze > hydrogen bonds, CG approximations are not probably sufficient. > > This is a good exercise in planning your analysis before conducting your > simulation. You can probably estimate some sort of polar contacts from your > CG > representation, but not hydrogen bonds. > > -Justin > > > On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi > > wrote: > >> Hi, > >> To change between representations (atomistic <--> coarse grained), if you > >> are using the MARTINI FF, you can use the modified version of Gromacs > 3.3, > >> check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt > >> If you don't want to switch to full-atomistic representation, check which > CG > >> atom types are able to form hydrogen bonds and look for interactions > between > >> them. Obviously, this will be an approximation. > >> > >> Esteban G. Vega-Hissi > >> UNSL > >> San Luis > >> Argentina > >> -- > >> On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson > > >> wrote: > >>> There are programs around for reconstruction of full-atomistic > >>> representations > >>> from coarse-grained representations, however. I don't know if there are > >>> any > >>> available for the GROMACS architecture. > >>> > >>> > >>> > >>> > >>> Quoting Nuno Azoia : > >>> > >>>> Hi there! > >>>> > >>>> I never worked with coarse grain simulations, but if you used a coarse > >>>> grain methodology you didn't include all the atoms, so you didn't > >>>> included hydrogens. So now you can not see them, of course. They are > not > >>>> there. > >>>> > >>>> If you need to "know the hydrogen bond interactions" you need to do > some > >>>> "all atoms" simulation, not coarse grain. > >>>> > >>>> Nuno Azoia > >>>> > >>>> On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote: > >>>>> Dear Gromacs Users, > >>>>> > >>>>> I have done coarse grain simulation for 2 peptides in bilayer for > >>>>> 1000ns, and now i would like to know the hydrogen bond interactions > >>>>> between these two peptides. Please let me know how to do this, i can > >>>>> visualize the trajectory in VMD, but unable to calculate the hydrogen > >>>>> bonding distance and the hydrogen bonds existing.. > >>>>> > >>>>> Thanks > >>>>> > >>>>> Ram > >>>> -- > >>>> Nuno Gonçalo Azoia Lopes > >>>> > >>>> Laboratório de Investigação em Acabamento > >>>> Departamento de Engenharia Têxtil > >>>> Universidade do Minho > >>>> Campus de Azurém > >>>> 4800-058 Guimarães > >>>> Portugal > >>>> > >>>> Tel: +351 253 510 280 - Ext: 517 289 > >>>> Fax: +351 253 510 293 > >>>> > >>>> Mobile: +351 965 382 487 > >>>> E-mail: naz...@det.uminho.pt > >>>> http://nazoia.net > >>>> > >>>> -- > >>>> gmx-users mailing listgmx-users@gromacs.org > >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>>> Please search the archive at http://www.gromacs.org/search before > >>>> p
Re: [gmx-users] coarse grain dynamics
There are programs around for reconstruction of full-atomistic representations from coarse-grained representations, however. I don't know if there are any available for the GROMACS architecture. Quoting Nuno Azoia : > Hi there! > > I never worked with coarse grain simulations, but if you used a coarse > grain methodology you didn't include all the atoms, so you didn't > included hydrogens. So now you can not see them, of course. They are not > there. > > If you need to "know the hydrogen bond interactions" you need to do some > "all atoms" simulation, not coarse grain. > > Nuno Azoia > > On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote: > > Dear Gromacs Users, > > > > I have done coarse grain simulation for 2 peptides in bilayer for > > 1000ns, and now i would like to know the hydrogen bond interactions > > between these two peptides. Please let me know how to do this, i can > > visualize the trajectory in VMD, but unable to calculate the hydrogen > > bonding distance and the hydrogen bonds existing.. > > > > Thanks > > > > Ram > > -- > Nuno Gonçalo Azoia Lopes > > Laboratório de Investigação em Acabamento > Departamento de Engenharia Têxtil > Universidade do Minho > Campus de Azurém > 4800-058 Guimarães > Portugal > > Tel: +351 253 510 280 - Ext: 517 289 > Fax: +351 253 510 293 > > Mobile: +351 965 382 487 > E-mail: naz...@det.uminho.pt > http://nazoia.net > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
re: [gmx-users] electro-static potential energy after minimization
> > > > > -- > > > > > > > > > > > > Justin A. Lemkul > > > > Ph.D. Candidate > > > > ICTAS Doctoral Scholar > > > > MILES-IGERT Trainee > > > > Department of Biochemistry > > > > Virginia Tech > > > > Blacksburg, VA > > > > jalemkul[at]vt.edu | (540) 231-9080 > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > > > > > > > -- > > > > 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/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/mailing_lists/users.php > > > > > > ---- > > > Hotmail: Trusted email with Microsofts powerful SPAM protection. Sign > > > up now. <https://signup.live.com/signup.aspx?id=60969> > > > > > > > -- > > > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > Hotmail: Free, trusted and rich email service. Get it now. > _ > Hotmail: Free, trusted and rich email service. > https://signup.live.com/signup.aspx?id=60969 -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Histrionic answers doesn't help!
Unfortunately Jhony, many users want a "black box" solution that magically makes answers appear without any grind. Few members in this community have the kind of time required to provide these solutions. Mark's reply was somewhat justified by the nature of the question. ~j Quoting Jhony Tolengo : > Mark Abraham and Gareth Tribello: > > Because of your embarrassing answers (this is abuse!) to mailing list users, > many of them simply will choose other sotware than Gromacs to simulate > systems. > > For you health, please don't reply, take both an anxiolytic of any kind or > take vacations! > > Peace. > > J.M.S. > -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] g_covar & g_anaeig problems
Greetings, I'm trying to use g_covar to generate a covariance matrix, followed by g_anaeig to analyze the data. The trajectory is a list of clusters generated by g_cluster in .trr format. gmxcheck seems to think that the input trajectory is fine but the cluster trajectory gives this error when gmxcheck is used: Timesteps at t=9974 don't match (2, 4) Timesteps at t=9978 don't match (4, 2) for every t += 4. g_covar crashes when I use my trajectory, giving the message: WARNING: number of atoms in tpx (730) and trajectory (730) do not match and then usually gives a segmentation fault message or a memory error. Help? best, Jared -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
