[gmx-users] Re:gmx-users Digest, Vol 113, Issue 54
Dear prof. after i calculating the secondary strucure of residues frome 20 to 60 using do_dssp . And then i use xpm2ps to show the picture with ps.m2p, but the residue order number of y-axis start form 1 not the 20. how can i change the order of residue? Thank you very much! At 2013-09-12 18:00:06,gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. RE: average pressure of a system (Dwey Kauffman) 2. how to make a index file (aixintiankong) 3. RE: RE: average pressure of a system (Dallas Warren) 4. Re: RE: average pressure of a system (Tsjerk Wassenaar) 5. PhD vacancy on MD modelling at University of Groningen (Patrick Onck) -- Message: 1 Date: Wed, 11 Sep 2013 20:31:50 -0700 (PDT) From: Dwey Kauffman mpi...@gmail.com Subject: [gmx-users] RE: average pressure of a system To: gmx-users@gromacs.org Message-ID: 1378956710192-5011137.p...@n6.nabble.com Content-Type: text/plain; charset=UTF-8 Justin Lemkul wrote On 9/11/13 12:12 AM, Dwey Kauffman wrote: True, but thermostats allow temperatures to oscillate on the order of a few K, and that doesn't happen on the macroscopic level either. Hence the small disconnect between a system that has thousands of atoms and one that has millions or trillions. Pressure fluctuations decrease on the order of sqrt(N), so the system size itself is a determining factor for the pressure fluctuations. As previous discussions have rightly concluded, pressure is a somewhat ill-defined quantity in molecular systems like these. Dose it also imply that it is not a good idea to study the relationship between dimer (multimer) dissociation and macroscopic pressure in this case ? (due to the ill defined pressure). I would simply think it would be very hard to draw any meaningful conclusions if they depend on a microscopic quantity that varies so strongly. It is hard to be justified if I assign a set of various ref_p= 0.7, 0.8, 0.9, 1.0, 1.1, 1.2 , perform independent simulations, and then obtain outcomes of targeted quantities for comparison. As with the original issue, I would find it hard to believe that any of the differences observed in such a setup would be meaningful. Is 0.7 ± 100 actually different from 1.2 ± 100? You could try altering tau_p, but I doubt there is any value in doing so. I would give it a try. This will really only change the relaxation time. Smaller values of tau_p may improve the average slightly, but may also (more likely) lead to instability, especially with Parrinello-Rahman. I carried out independent NPT processes with different tau_p values = 1.5, 1.0 and 0.5 ## tau_p 1.5 Energy Average Err.Est. RMSD Tot-Drift --- Pressure2.628592.6 185.682.67572 (bar) ## tau_p 1.0 Energy Average Err.Est. RMSD Tot-Drift --- Pressure 0.8867691.7187.737 0.739 (bar) ## tau_p 0.5 Energy Average Err.Est. RMSD Tot-Drift --- Pressure2.399112.2185.708 6.8189 (bar) ## It is clear that when tau_p =1.0, average pressure of the system (=0.89 bar) is close to ref_p =1.0 bar However, it is unclear to me as to how to assign a good value to tau_p in order to reach at a close value of ref_p. As shown above, both of the average pressures as tau_p =1.5 and 0.5 are much higher than that as tau_p =1.0. A smaller tau_p may or may not help. Another issue caused by system pressure is about pbc box size. Since I use pressure coupling, the box size is not fixed such that protein moved away the center of membrane for a long simulation like 30 ns. Box size changes significantly during production MD. Is there a way to fix the box size at the very beginning ? although turning off pressure coupling will make box size fixed. Best regards, Dwey -- View this message in context: http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system-tp5011095p5011137.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Message: 2 Date:
[gmx-users] SD integrator
Hi all, I have been posting for a while with my problems in simulating peptides inside CNTs. After a lot of trials it seems like simulating the CNT with bonds and angles seems like a wise thing to do. I am using the SD integrator + PR barostat. It seems like improper thermostatting can blow up the system. For example, when I am trying to simulate with tau-t for CNT as 1.0 the system blows up for 300K. The output temperatures (from g_energy) for CNT is about 150K for a ref-t of 300K. However, if a stronger coupling is used tau-t = 0.005, the system works fine. Are there any artifacts for coupling the CNT group with such a low tau-t? -- 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
Fwd: [gmx-users] SD integrator
There must be some problem with degrees of freedom in your system... Dr. Vitaly V. Chaban -- Forwarded message -- From: HANNIBAL LECTER hanniballecte...@gmail.com Date: Fri, Sep 13, 2013 at 7:15 PM Subject: [gmx-users] SD integrator To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all, I have been posting for a while with my problems in simulating peptides inside CNTs. After a lot of trials it seems like simulating the CNT with bonds and angles seems like a wise thing to do. I am using the SD integrator + PR barostat. It seems like improper thermostatting can blow up the system. For example, when I am trying to simulate with tau-t for CNT as 1.0 the system blows up for 300K. The output temperatures (from g_energy) for CNT is about 150K for a ref-t of 300K. However, if a stronger coupling is used tau-t = 0.005, the system works fine. Are there any artifacts for coupling the CNT group with such a low tau-t? -- 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] Re: Gromacs: GPU detection
FYI, I've file a bug report which you can track if interested: http://redmine.gromacs.org/issues/1334 -- Szilárd On Sun, Sep 1, 2013 at 9:49 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: I may have just come across this issue as well. I have no time to investigate, but my guess is that it's related to some thread-safety issue with thread-MPI. Could one of you please file a bug report on redmine.gromacs.org? Cheers, -- Szilárd On Thu, Aug 8, 2013 at 5:52 PM, Brad Van Oosten bv0...@brocku.ca wrote: I can confirm this, I have noticed this as well. -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-GPU-detection-tp5010308p5010399.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 -- 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] MD simulations of Tyrosinase using GROMACS
Dear GMX users, I am trying to carry out MD simulations with tyrosinase protein. Tyrosinase is a tyoe-3 copper protein. In its oxygen binding active site, the protein has two copper atoms that bind to two oxygen atoms in a peroxo configuration. Each copper is co-ordinated by three histidine residues. While I am trying to generate a topology file for the protein I always get an error message showing CU is not recognized by any force field. This pretty clear that Copper is not parameterized by any of the force fields. Could any one hep me in this regard by including Copper parameters into the force field and also defining the bonds between Copper - Oxygen and Copper Histidine. If any one has carried out MDS in similar lines please help me in this regard. Thanking you. -- View this message in context: http://gromacs.5086.x6.nabble.com/MD-simulations-of-Tyrosinase-using-GROMACS-tp5011165.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
Re: Fwd: [gmx-users] SD integrator
Do you couple CNT as a separate T-group? It should be done so. I think your systems blows up because of incorrectly defined bonded parameters for the tube, not due to thermostatting. For instance, you might not define all the valence angles and dihedrals. See my papers for the parameters for CNT, if you need such... Dr. Vitaly V. Chaban On Fri, Sep 13, 2013 at 8:55 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: However, even if position restraints are not used, the error can be reproduced. I am constraining the bonds in my CNTs though. I was wondering if you could point me to some parameters for CNT. On Fri, Sep 13, 2013 at 1:50 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: I am position restraining the CNT group. That affects the degrees of freedom. On Sep 13, 2013 1:43 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: There must be some problem with degrees of freedom in your system... Dr. Vitaly V. Chaban -- Forwarded message -- From: HANNIBAL LECTER hanniballecte...@gmail.com Date: Fri, Sep 13, 2013 at 7:15 PM Subject: [gmx-users] SD integrator To: Discussion list for GROMACS users gmx-users@gromacs.org Hi all, I have been posting for a while with my problems in simulating peptides inside CNTs. After a lot of trials it seems like simulating the CNT with bonds and angles seems like a wise thing to do. I am using the SD integrator + PR barostat. It seems like improper thermostatting can blow up the system. For example, when I am trying to simulate with tau-t for CNT as 1.0 the system blows up for 300K. The output temperatures (from g_energy) for CNT is about 150K for a ref-t of 300K. However, if a stronger coupling is used tau-t = 0.005, the system works fine. Are there any artifacts for coupling the CNT group with such a low tau-t? -- 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 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] Distance calculation
Hi , I there any tool to calculate distance between particular atom from one group(protein) to particular atom from another group(DMPC lipid in Bilayer). For Example: protein backbone Amide(HN) to acyl chain carbon atom(C2D) in DMPC lipid. Thanks Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-calculation-tp5011170.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
Re: [gmx-users] how to make a index file
Please don't reply to the entire digest. On 9/13/13 9:25 AM, aixintiankong wrote: Dear prof. after i calculating the secondary strucure of residues frome 20 to 60 using do_dssp . And then i use xpm2ps to show the picture with ps.m2p, but the residue order number of y-axis start form 1 not the 20. how can i change the order of residue? Thank you very much! Renumber them in a text editor. -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
