[gmx-users] Ligand simulation
Dear users, Although this topic has been extensively discussed in the list previously, I am unclear about the solution for the problem.. While running ligand in water simulation (EM) with RF-0 I get the following message: -- Number of degrees of freedom in T-Coupling group rest is 24531.00 Largest charge group radii for Van der Waals: 0.458, 0.356 nm Largest charge group radii for Coulomb: 0.458, 0.356 nm NOTE 1 [file ../em.mdp]: The sum of the two largest charge group radii (0.814337) is larger than rlist (1.60) - rvdw (1.00) NOTE 2 [file ../em.mdp]: The sum of the two largest charge group radii (0.814337) is larger than rlist (1.60) - rcoulomb (1.40) -- But I continued for nvt and npt where I got the same notes NVT - -- Largest charge group radii for Van der Waals: 0.509, 0.487 nm Largest charge group radii for Coulomb: 0.509, 0.487 nm NOTE 1 [file ../nvt.mdp]: The sum of the two largest charge group radii (0.996343) NOTE 2 [file ../nvt.mdp]: The sum of the two largest charge group radii (0.996343) . -- for NPT - Number of degrees of freedom in T-Coupling group System is 16357.00 Largest charge group radii for Van der Waals: 0.787, 0.684 nm Largest charge group radii for Coulomb: 0.787, 0.684 nm NOTE 1 [file ../npt.mdp]: The sum of the two largest charge group radii (1.470764) . NOTE 2 [file ../npt.mdp]: The sum of the two largest charge group radii (1.470764) . -- For MD - -- Largest charge group radii for Van der Waals: 0.671, 0.605 nm Largest charge group radii for Coulomb: 0.671, 0.605 nm NOTE 1 [file md.mdp]: The sum of the two largest charge group radii (1.276104) .. NOTE 2 [file md.mdp]: The sum of the two largest charge group radii (1.276104) . -- The ligand is not broken, whole of it is inside the water in the beginning of the simulation, topology is ok because protein-ligand simulation with PME ran fine. Any suggestions are welcome. Thank you Regards kavya -- 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_lie and ligand only simulation
Dear users, Sorry for repeating the same question. I just wanted to know whether is it ok if I have rlist rcoulomb in ligand-water and prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb in the original simulation using PME? Thank you Regards Kavya On Wed, Nov 6, 2013 at 11:52 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, When the simulation was carried out with PME rcoulomb was set equal to rlist. But when I need to to ligand-water simulation without PME (with RF-0) then it requires rlist greater by 0.1-0.3 than rcoulomb. So if I rerun protein-ligand-water simulation there could be more differences in the energies isnt it? Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:51 PM, Kavyashree M hmkv...@gmail.com wrote: Ok thank you. I thought it was for protein-ligand-water that needs to be rerun without PME. Thanks Regards Kavya On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 12:14 PM, Kavyashree M wrote: Sir, Thank you. Should the ligand-water MD be done without PME? I already answered this. Please read my previous reply again. -Justin Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done with PME, then the energies recalculated using mdrun -rerun without PME. More detailed methods are available in the list archive; this topic gets discussed a lot. -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 -- == 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 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_lie and ligand only simulation
Thank you.. On Wed, Nov 6, 2013 at 7:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/6/13 5:47 AM, Kavyashree M wrote: Dear users, Sorry for repeating the same question. I just wanted to know whether is it ok if I have rlist rcoulomb in ligand-water and prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb in the original simulation using PME? The energies are inherently going to be different because you are evaluating nonbonded energies with different methods. Typically, I think people just use long cutoffs for the recalculation. -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 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_lie and ligand only simulation
Dear users, When the simulation was carried out with PME rcoulomb was set equal to rlist. But when I need to to ligand-water simulation without PME (with RF-0) then it requires rlist greater by 0.1-0.3 than rcoulomb. So if I rerun protein-ligand-water simulation there could be more differences in the energies isnt it? Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:51 PM, Kavyashree M hmkv...@gmail.com wrote: Ok thank you. I thought it was for protein-ligand-water that needs to be rerun without PME. Thanks Regards Kavya On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 12:14 PM, Kavyashree M wrote: Sir, Thank you. Should the ligand-water MD be done without PME? I already answered this. Please read my previous reply again. -Justin Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done with PME, then the energies recalculated using mdrun -rerun without PME. More detailed methods are available in the list archive; this topic gets discussed a lot. -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 -- == 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 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_lie and ligand only simulation
Sir, Thank you. Should the ligand-water MD be done without PME? Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done with PME, then the energies recalculated using mdrun -rerun without PME. More detailed methods are available in the list archive; this topic gets discussed a lot. -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 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_lie and ligand only simulation
Ok thank you. I thought it was for protein-ligand-water that needs to be rerun without PME. Thanks Regards Kavya On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 12:14 PM, Kavyashree M wrote: Sir, Thank you. Should the ligand-water MD be done without PME? I already answered this. Please read my previous reply again. -Justin Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done with PME, then the energies recalculated using mdrun -rerun without PME. More detailed methods are available in the list archive; this topic gets discussed a lot. -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 -- == 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 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_lie and ligand only simulation
Dear Gromacs users, I have a protein-ligand in water simulation (Gmx 4.5.3), for calculating free energy of ligand binding, a separate simulation of ligand in water simulation is required (which I read from the list). The question is the protein-ligand is simulated as a dimeric system so is it necessary to simulate the ligand in water as a dimer too. Please clarify. Thank you Regards Kavya -- 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_lie and ligand only simulation
Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? Thank you Regards kavya -- 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] Writing periodic image coordinates.
Dear users, For some analysis I require the 27 periodic images of the system I ran the simulation for. Kindly let me know how can it be written to a pdb file. Thanking you Regards Kavya -- 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] Writing periodic image coordinates.
Thank you Sir! Regards Kavya On Fri, Sep 27, 2013 at 12:52 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Kavya, genconf -nbox 3 3 3 Cheers, Tsjerk On Thu, Sep 26, 2013 at 6:24 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For some analysis I require the 27 periodic images of the system I ran the simulation for. Kindly let me know how can it be written to a pdb file. Thanking you Regards Kavya -- 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 -- 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] The sum of the two largest charge group radii ..is larger than rlist
Dear users, After EM step while running NVT I gor a warning saying - Largest charge group radii for Van der Waals: 3.798, 1.293 nm Largest charge group radii for Coulomb: 7.565, 3.798 nm The sum of the two largest charge group radii (11.362685) is larger than rlist (1.40) But this error was not there while EM - Largest charge group radii for Van der Waals: 0.039, 0.039 nm Largest charge group radii for Coulomb: 0.084, 0.084 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 100x100x100, spacing 0.119 0.119 0.119 I was not able to check this error in mailing list as the page was not opening. Kindly help. Thank you Regards Kavya -- 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] The sum of the two largest charge group radii ..is larger than rlist
Ok Thank you. Regards Kavya On Tue, Aug 6, 2013 at 3:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/6/13 2:35 AM, Kavyashree M wrote: Dear users, After EM step while running NVT I gor a warning saying - Largest charge group radii for Van der Waals: 3.798, 1.293 nm Largest charge group radii for Coulomb: 7.565, 3.798 nm The sum of the two largest charge group radii (11.362685) is larger than rlist (1.40) But this error was not there while EM - Largest charge group radii for Van der Waals: 0.039, 0.039 nm Largest charge group radii for Coulomb: 0.084, 0.084 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 100x100x100, spacing 0.119 0.119 0.119 I was not able to check this error in mailing list as the page was not opening. Everything on the Gromacs site appears to be working now. The explanation is given on the error page. If you're not using Gromacs 4.6.3, upgrade - there is a possibility this is a small bug that has already been fixed. -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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] concatenating 2 xtc files
Sir, But if something went wrong, then over is rather irrelevant, isn't it? Yes. I am planning to rerun ifI dont get any solution. So your simulation started from some previous point and re-ran? I don't see how this would be possible given what you have been posting. The overlap was because. Even though I continued from the ~5ns in 64 cores I had run a little longer in 8 core machine. AS the job was in queue for a long period. That's why I asked before about checking the contents of the .tpr file. You need to verify what it is exactly that you're doing and identify sources of potential problems. Thank you Regards Kavya -- 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] concatenating 2 xtc files
Dear users, I ran a simulation for 25ns. First 5ns in 8 core machine and late part in 64 cores. It ran without any problem. The trajectories were concatenated, jumps are removed and rmsd was calculated. But there was sudden jump in the rmsd curve. Is it wrong to run simulations in different cores like this? Thank you Regards Kavya -- 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] concatenating 2 xtc files
Dear Sir, First trajectory - traj1.xtc (0 to 5... ns) Second trajectory - traj2.xtc (5... to 25ns) But there is no gap in between. for concatenating - $ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc For nujump - $ trjconv -f trajf.xtc -s md.tpr -pbc nojump -o trajf.xtc I also have a case where I ran 10ns in 64 cores and later continued in 8core machine. This also has the same problem. While running in 64 cores by default it did not generate the checkpoint file. So I has to use tpbconv to generate a new tpr file for continuing from the same point - $ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr Thanks in advance. Regards Kavya On Thu, Aug 1, 2013 at 12:20 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Kavya, That shouldn be a problem. Please post your sequence of commands for concatenating and further processing of the trajectory. Cheers, Tsjerk On Thu, Aug 1, 2013 at 8:12 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I ran a simulation for 25ns. First 5ns in 8 core machine and late part in 64 cores. It ran without any problem. The trajectories were concatenated, jumps are removed and rmsd was calculated. But there was sudden jump in the rmsd curve. Is it wrong to run simulations in different cores like this? Thank you Regards Kavya -- 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 -- 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] concatenating 2 xtc files
Sir, Thank you for the suggestion.. I will make use of it in future runs. but now the simulation is over. There was some overlap of few ns in 8core machine. so while checking the rmsd plot there was a significant difference in rmsd between 8 core and 64 core overlapped region of simulation. 1 more question is suppose I do not have checkpoint file and if I need to continue from a stopped point (not extending) does this command do the job? $ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr Because when I tried with this there was a jump in the rmsd Thank you Regards Kavya On Thu, Aug 1, 2013 at 5:18 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/1/13 3:42 AM, Kavyashree M wrote: Dear Sir, First trajectory - traj1.xtc (0 to 5... ns) Second trajectory - traj2.xtc (5... to 25ns) But there is no gap in between. for concatenating - $ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc For nujump - $ trjconv -f trajf.xtc -s md.tpr -pbc nojump -o trajf.xtc I also have a case where I ran 10ns in 64 cores and later continued in 8core machine. This also has the same problem. While running in 64 cores by default it did not generate the checkpoint file. So I has to use tpbconv to generate a new tpr file for continuing from the same point - $ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr I would suggest using gmxdump on new.tpr to verify that the coordinates it contains are the same as the last frame in traj.trr. -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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] creating a checkpoint file
Dear users, For some unknown reasons checkpoint file are not being created if -cpo is not mentioned (in 4.5.3). Now I have a trajectory of ~10ns without a checkpoint file. I tried the following - tpbconv option to create a new .tpr file so that I can start form the point I stopped. But manual mentions the cpt file has to be used. So my question is - 1. Is it ok if I us the new tpr file created using tpbconv to continue the simulation 2. If not how can I create a checkpoint file now? Thank you Regards Kavya -- 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] Initial cell size is smaller than the cell size limit..
Dear users, While running a ligand bound MD using AMber03 force field. I got the following error after ~ 4.9 ns The initial cell size (1.247705) is smaller than the cell size limit (1.586683), change options -dd, -rdd or -rcon, see the log file for details Initially I ran using 64 nodes (till 3.3ns). later on I shifted the trajectory to another machine and ran using 8 cores. It ran fine till 4.926ns. Suddenly it stopped with the above error. Kindly provide some guidance. Thank you Regards Kavya -- 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] Salt bridge observation
Sir, Why I mentioned NH2 CG saltbridge because the g_saltbr gives the charge group and does not mention the OD2 of ASP but mentions only CG. Otherwise it does not make any sense. Thanks Regards Kavya On Thu, Apr 4, 2013 at 1:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/4/13 12:27 AM, Kavyashree M wrote: Sir, That is true, previously you had explained regarding this. Calculation using g_saltbr 1. For g_saltbr I included the following residues - ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated which contained only these residues. sb was calculated using - g_saltbr -f traj.xtc -s md.tpr -b 4000 -e 4000 -t 0.4 -sep 2. Files that were generated were filtered and only those having sb between ASP, GLU and ARG LYS were retained. 3. Further, out of these sbs, those which had the following atoms CG ASP, CD GLU, NE ARG, NH1 ARG, NH2 ARG, NZ LYS were retained. Calculation using g_hbond - It was done using the index file mentioned in my previous post using g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm -hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000 So essentially the final results in both are composed of sbs formed between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr while charged atoms in case of g_hbond. The comparison showed that all sbs from g_hbond were present in the output from g_saltbr. But g_saltbr had some additional sbs off-course between the same charged groups. But only the distance was greater than 4 Ang for ex- distance between NH2 ARG and OD2 ASP is 4.32Ang Since it considers charged group CG of ASP instead of OD2 ASP distance between NH2 ARG and CG ASP is 5.54 Ang So g_saltbr is doing something weird, though I don't see how it is possible to be honest. It's up to you to filter the information by what you believe to be useful. An NH2-CG salt bridge likely doesn't make any sense at all, anyway. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Salt bridge observation
Ok. Still the distance is beyond the mentioned cut-off. The distance of both OD1 and OD2 of ASP is more than 4 Ang from NH2 of Arg. Thank you Regards Kavya On Thu, Apr 4, 2013 at 2:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/4/13 4:34 AM, Kavyashree M wrote: Sir, Why I mentioned NH2 CG saltbridge because the g_saltbr gives the charge group and does not mention the OD2 of ASP but mentions only CG. Otherwise it does not make any sense. Now I remember how g_saltbr naming works. It measured distances between charge groups, and the file names are based on the first atom in the charge group, so CG indicates the gamma-carboxylate group of ASP, which includes both OD1 and OD2. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Salt bridge observation
Dear users, This is regarding an observation while calculating the salt bridge (sb) using g_saltbr. I used g_saltbr and g_hbond (with contact option) with a cut of of 4Ang, for calculating sb in the whole protein at a single frame. I made sure that I considered sb between same set of residues (ASP, GLU with LYS ARG) in both calculations. and filtered accordingly. While checking the individual sb it was found that most of the results from g_saltbr matches with g_hbond but g_saltbr gives some extra sbs. On checking these extra sb it was found that the distance between the atoms forming sb are more than the cut of I had mentioned (4 Ang). Not sure why it is like this. But just wanted to convey this observation. Thank you regards Kavya -- 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] Salt bridge observation
Sir, That is true, previously you had explained regarding this. Calculation using g_saltbr 1. For g_saltbr I included the following residues - ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated which contained only these residues. sb was calculated using - g_saltbr -f traj.xtc -s md.tpr -b 4000 -e 4000 -t 0.4 -sep 2. Files that were generated were filtered and only those having sb between ASP, GLU and ARG LYS were retained. 3. Further, out of these sbs, those which had the following atoms CG ASP, CD GLU, NE ARG, NH1 ARG, NH2 ARG, NZ LYS were retained. Calculation using g_hbond - It was done using the index file mentioned in my previous post using g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm -hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000 So essentially the final results in both are composed of sbs formed between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr while charged atoms in case of g_hbond. The comparison showed that all sbs from g_hbond were present in the output from g_saltbr. But g_saltbr had some additional sbs off-course between the same charged groups. But only the distance was greater than 4 Ang for ex- distance between NH2 ARG and OD2 ASP is 4.32Ang Since it considers charged group CG of ASP instead of OD2 ASP distance between NH2 ARG and CG ASP is 5.54 Ang There are some 10 more such examples. I can send the calculations if requires. Thank you Regards Kavya On Wed, Apr 3, 2013 at 10:25 PM, Justin Lemkul jalem...@vt.edu wrote: On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, This is regarding an observation while calculating the salt bridge (sb) using g_saltbr. I used g_saltbr and g_hbond (with contact option) with a cut of of 4Ang, for calculating sb in the whole protein at a single frame. I made sure that I considered sb between same set of residues (ASP, GLU with LYS ARG) in both calculations. and filtered accordingly. While checking the individual sb it was found that most of the results from g_saltbr matches with g_hbond but g_saltbr gives some extra sbs. On checking these extra sb it was found that the distance between the atoms forming sb are more than the cut of I had mentioned (4 Ang). Not sure why it is like this. But just wanted to convey this observation. Please provide a concrete example. Note that running g_saltbr and g_hbond (with the index files mentioned before) should not be expected to produce equivalent result. g_saltbr is relatively stupid; it considers any group with a charge ± 0.2 to be capable of participating in a salt bridge. In some cases, this will include methylene groups or others than are near the actual charged groups. Such behavior could easily account for whatever observation you're making. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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] Re: Salt bridge Calculations
Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- 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: Salt bridge Calculations
Sir, Thank you very much for your reply. I wanted to calculate Salt bridge in the whole protein so i am not mentioning the residues involved. The problem with g_saltbr was that if I have to calculate the accessibility of these atoms it will be a problem because it gives the charge groups but not exact atoms. This is the reason I thought of using g_hbond. But I wanted clarification from experts in using this method. So Is there any problem if I use g_hbond? Thank you kavya On Tue, Apr 2, 2013 at 9:03 PM, bipin singh bipinel...@gmail.com wrote: You can use g_dist with specific atoms indices to calculate distances, if you already have the information about atoms involved in salt bridge interactions. On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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: Salt bridge Calculations
Sir, This g_hbond will generate a matrix similar to what g_saltbr would have given in terms of variation of distance between two charge groups. I want to find out the variation of all the salt bridges in the protein over the trajectory, if I have to use g_dist with an index of positive atoms and another of negative atoms, then it will calculate the distance between the centre of mass of these two groups.. according to manual. So How can I use g_dist for this kind of calculation. I am little confused. If I take a cut of of 0.4nm (as we mention in g_saltbr), will it be wrong if I have to calculate salt bridges between these two indices - group 1: ASP_GLU__OD1_OD2_OE1_OE2 group 2: ARG_LYS__NZ_NE_NH1_NH2 Thank you Kavya On Tue, Apr 2, 2013 at 10:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 11:58 AM, Kavyashree M wrote: Sir, Thank you very much for your reply. I wanted to calculate Salt bridge in the whole protein so i am not mentioning the residues involved. The problem with g_saltbr was that if I have to calculate the accessibility of these atoms it will be a problem because it gives the charge groups but not exact atoms. This is the reason I thought of using g_hbond. But I wanted clarification from experts in using this method. So Is there any problem if I use g_hbond? Does this really give you any useful information? You'll get an output file with putative contacts derived from an arbitrary cutoff for any possible positive-negative pair defined in the index group. I think the g_dist approach is far more useful and gives you exact insight into specific pairs. It takes a bit more prep work, but looping the calculations is trivial to do to make them efficient. -Justin Thank you kavya On Tue, Apr 2, 2013 at 9:03 PM, bipin singh bipinel...@gmail.com wrote: You can use g_dist with specific atoms indices to calculate distances, if you already have the information about atoms involved in salt bridge interactions. On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
Re: [gmx-users] Re: Salt bridge Calculations
Sir, Thank you for the detailed insight. As you mentioned It does not give much information. But the matrix that it would generate would only show whether a specific salt bridge (SB) exited at a given time within the cut-off (0.4). I got your explanation. Yes water mediated SBs are also interesting. If I had a given set of known SB then I would have definitely gone for g_dist. Thank you very much. Kavya On Tue, Apr 2, 2013 at 10:45 PM, Justin Lemkul jalem...@vt.edu wrote: On Tue, Apr 2, 2013 at 1:09 PM, Kavyashree M hmkv...@gmail.com wrote: Sir, This g_hbond will generate a matrix similar to what g_saltbr would have given in terms of variation of distance between two charge groups. I suppose, in that sense, the output can be useful. I want to find out the variation of all the salt bridges in the protein over the trajectory, if I have to use g_dist with an index of positive atoms and another of negative atoms, then it will calculate the distance between the centre of mass of these two groups.. according to manual. Yes, but that's not what I suggested you do. You would need an index group for each residue individually, not all negative atoms and all positive atoms. That would definitely be useless. If you consider each residue individually, you can get a very detailed look at what's going on. What you're doing now is saying a salt bridge exists if N and O atoms are within 0.4 nm. Is that an accurate descriptor? Upon what precedent have you based that assessment? g_dist will also show you frames where those atoms may not be within 0.4 nm, but what about the case of water-mediated interactions; are those not interesting, as well? What I think you should be doing is approaching the problem from multiple perspectives to get a real look at what's going on. -Justin So How can I use g_dist for this kind of calculation. I am little confused. If I take a cut of of 0.4nm (as we mention in g_saltbr), will it be wrong if I have to calculate salt bridges between these two indices - group 1: ASP_GLU__OD1_OD2_OE1_OE2 group 2: ARG_LYS__NZ_NE_NH1_NH2 Thank you Kavya On Tue, Apr 2, 2013 at 10:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/2/13 11:58 AM, Kavyashree M wrote: Sir, Thank you very much for your reply. I wanted to calculate Salt bridge in the whole protein so i am not mentioning the residues involved. The problem with g_saltbr was that if I have to calculate the accessibility of these atoms it will be a problem because it gives the charge groups but not exact atoms. This is the reason I thought of using g_hbond. But I wanted clarification from experts in using this method. So Is there any problem if I use g_hbond? Does this really give you any useful information? You'll get an output file with putative contacts derived from an arbitrary cutoff for any possible positive-negative pair defined in the index group. I think the g_dist approach is far more useful and gives you exact insight into specific pairs. It takes a bit more prep work, but looping the calculations is trivial to do to make them efficient. -Justin Thank you kavya On Tue, Apr 2, 2013 at 9:03 PM, bipin singh bipinel...@gmail.com wrote: You can use g_dist with specific atoms indices to calculate distances, if you already have the information about atoms involved in salt bridge interactions. On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 http://www.gromacs.org/Support/Mailing_Lists -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users
[gmx-users] Salt bridge Calculations
Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- 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] Free energy landscape by g_sham
Thank you Sir Regards kavya On Sun, Mar 31, 2013 at 11:58 AM, bipin singh bipinel...@gmail.com wrote: g_sham calculates free energy landscapes by computing the joint probability distribution from the two dimensional plane constructed using two quantities (in your case it will be rmsd and radius of gyration). Conformations sampled during the simulation were projected on this two dimensional plane, and the number of points occupied by each cell was counted. The grid cell containing the maximum number of points is then assigned as the reference cell, with a free energy value of zero. Free energies for all the other cells were assigned with respect to this reference cell using the following equation: ΔG = -kbT ln P(x,y)/Pmin P(x,y) is the estimate of probability density function obtained from a histogram of MD data and Pmin is the maximum of the probability density function. Kb is the Boltzmann constant, and T is the temperature corresponding to each simulation. On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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] Free energy landscape by g_sham
Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- 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] Hydrophobic contact cut-off
Dear users, Sorry for an off-topic question.. What is the distance cut-off considered for hydrophobic contact in protein? Some paper states 4-8Ang, while some other considers only till 5Ang. It is reported that this is a long range interaction. Any information clarifying this doubt will be very useful. Thank you Kavya -- 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] Hydrogen bonding differences
Dear Users, As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds. Still the Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen bond. Is there any other solution? Thank you Kavya On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M hmkv...@gmail.com wrote: Dear Sir, Sure I will try with 4.6. presently I am not able to download it. Thank you kavya On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund er...@xray.bmc.uu.sewrote: There were a handful of bugfixes to g_hbond over the last year. Could you try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form before. Erik On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote: Dear Sir, This is 4.5.3. I have not tried nomerge. I did not use nomerge option in any of them, So if it has counted it (Hbond b/w same donor and acceptor but with different hydrogen) twice in one calculation then it will be counted twice in another, So wont the result with/without nomerge be the same? The difference is 4-5 Hbonds.. Thank you Kavya On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi. What version was this? Have you tried with -nomerge? Erik On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: Dear users, While calculating hydrogen bonds for a simulation, it was found that the average number of intra protein hbonds was not equal to sum of MM, MS and SS hydrogen bonds. (MM - main chain - main chain, MS - main chain - side chain and side chain - side chain hydrogen bonds). There was a difference of 5 or so hbonds between intra-protein and MM+MS+SS hbonds. why is this so? I selected the options 7 7 for MM, 7 8 for MS and 8 8 for SS hydrogen bonds. One clarification. nhbdist option gives 0, 1, 2, 3 and total hydrogen bonds per hydrogen. Does this mean that a single hydrogen involving in forming hbond with 2 different acceptors/donors at different points of time in the trajectory. Thanks kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://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
Re: [gmx-users] Hydrogen bonding differences
Sir, I tried -nomerge. It is fine now. But will it be wrong to calculate without nomerge option? Thank you Kavya On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I could see how -merge (on by default) could lead to this. Have you tried -nomerge? Erik On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote: Dear Users, As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds. Still the Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen bond. Is there any other solution? Thank you Kavya On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M hmkv...@gmail.com wrote: Dear Sir, Sure I will try with 4.6. presently I am not able to download it. Thank you kavya On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There were a handful of bugfixes to g_hbond over the last year. Could you try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form before. Erik On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote: Dear Sir, This is 4.5.3. I have not tried nomerge. I did not use nomerge option in any of them, So if it has counted it (Hbond b/w same donor and acceptor but with different hydrogen) twice in one calculation then it will be counted twice in another, So wont the result with/without nomerge be the same? The difference is 4-5 Hbonds.. Thank you Kavya On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi. What version was this? Have you tried with -nomerge? Erik On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: Dear users, While calculating hydrogen bonds for a simulation, it was found that the average number of intra protein hbonds was not equal to sum of MM, MS and SS hydrogen bonds. (MM - main chain - main chain, MS - main chain - side chain and side chain - side chain hydrogen bonds). There was a difference of 5 or so hbonds between intra-protein and MM+MS+SS hbonds. why is this so? I selected the options 7 7 for MM, 7 8 for MS and 8 8 for SS hydrogen bonds. One clarification. nhbdist option gives 0, 1, 2, 3 and total hydrogen bonds per hydrogen. Does this mean that a single hydrogen involving in forming hbond with 2 different acceptors/donors at different points of time in the trajectory. Thanks kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search**h**ttp://www.gromacs.org/**Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/Support/**Mailing_Lists http:/**/www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search**h**ttp://www.gromacs.org/**Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/Support/**Mailing_Lists http:/**/www.gromacs.org/Support/**Mailing_Listshttp
Re: [gmx-users] Hydrogen bonding differences
Thank you Sir for clarifying the confusion. Regards kavya On Fri, Mar 22, 2013 at 11:18 PM, Erik Marklund er...@xray.bmc.uu.sewrote: I wouldn't say wrong, but I realized that some residue may make two hbonds to different parts of the protein, i.e. to the main chain and to a side chain at the same time. With -merge this counts as one if you analyze the entire protein. If you split your analysis such hbonds will show up in both e.g. SS and MS, hence TOT MM+SS+MS. It's just another way of counting hbonds. Erik On Mar 22, 2013, at 5:32 PM, Kavyashree M wrote: Sir, I tried -nomerge. It is fine now. But will it be wrong to calculate without nomerge option? Thank you Kavya On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I could see how -merge (on by default) could lead to this. Have you tried -nomerge? Erik On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote: Dear Users, As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds. Still the Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen bond. Is there any other solution? Thank you Kavya On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M hmkv...@gmail.com wrote: Dear Sir, Sure I will try with 4.6. presently I am not able to download it. Thank you kavya On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There were a handful of bugfixes to g_hbond over the last year. Could you try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form before. Erik On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote: Dear Sir, This is 4.5.3. I have not tried nomerge. I did not use nomerge option in any of them, So if it has counted it (Hbond b/w same donor and acceptor but with different hydrogen) twice in one calculation then it will be counted twice in another, So wont the result with/without nomerge be the same? The difference is 4-5 Hbonds.. Thank you Kavya On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi. What version was this? Have you tried with -nomerge? Erik On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: Dear users, While calculating hydrogen bonds for a simulation, it was found that the average number of intra protein hbonds was not equal to sum of MM, MS and SS hydrogen bonds. (MM - main chain - main chain, MS - main chain - side chain and side chain - side chain hydrogen bonds). There was a difference of 5 or so hbonds between intra-protein and MM+MS+SS hbonds. why is this so? I selected the options 7 7 for MM, 7 8 for MS and 8 8 for SS hydrogen bonds. One clarification. nhbdist option gives 0, 1, 2, 3 and total hydrogen bonds per hydrogen. Does this mean that a single hydrogen involving in forming hbond with 2 different acceptors/donors at different points of time in the trajectory. Thanks kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users ht**tp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users h**ttp://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/**mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/ Support/** http://www.gromacs.org/**Support/** http://www.gromacs.**org/Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://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_Listshttp://**www.gromacs.org/Support/** Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/**Support/**Mailing_Lists http:/**/www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/**Support/**Mailing_Lists
[gmx-users] query regarding mk_angndx
-- Forwarded message -- From: Kavyashree M hmkv...@gmail.com Date: Fri, Mar 8, 2013 at 10:45 PM Subject: query regarding mk_angndx To: Discussion list for GROMACS users gmx-users@gromacs.org Dear users, I used mkang_ndx to create an index file with dihedral angles. Input was: mk_angndx -s a.tpr -n angle.ndx -type dihedral output angle.ndx read like this - [ Phi=180.0_2_43.93 ] 52018192237353627323031 395957586176747566716970 ... According to my understanding the numbers indicate the 4 atoms defining the particular dihedral angle. But when I checked the pdb file for these atoms- ATOM 5 CA MET A 1 111.430 40.170 113.130 1.00 0.00 ATOM 18 C MET A 1 112.060 41.020 112.030 1.00 0.00 ATOM 19 O MET A 1 111.910 42.240 112.010 1.00 0.00 ATOM 20 N GLN A 2 112.940 40.430 111.220 1.00 0.00 I could not make out how this defines phi? Kindly clarify my confusion. Thank you kavya -- 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] query regarding mk_angndx
Dear users, I used mkang_ndx to create an index file with dihedral angles. Input was: mk_angndx -s a.tpr -n angle.ndx -type dihedral output angle.ndx read like this - [ Phi=180.0_2_43.93 ] 52018192237353627323031 395957586176747566716970 ... According to my understanding the numbers indicate the 4 atoms defining the particular dihedral angle. But when I checked the pdb file for these atoms- ATOM 5 CA MET A 1 111.430 40.170 113.130 1.00 0.00 ATOM 18 C MET A 1 112.060 41.020 112.030 1.00 0.00 ATOM 19 O MET A 1 111.910 42.240 112.010 1.00 0.00 ATOM 20 N GLN A 2 112.940 40.430 111.220 1.00 0.00 I could not make out how this defines phi? Kindly clarify my confusion. Thank you kavya -- 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_hbond and contact
Sir, I used gromacs 4.6. I got the point - index file will tell how many contacts an atom has made during the trajectory. Whether it has made a contact with an atom only in once or all the time, in the whole trajectory, it will be mentioned. Am I right? So from the problem I had, can I say that no. of contact/atom had increased in S2 while the no. of contact/time decreased? Its a bit confusing though! Thank you kavya On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund er...@xray.bmc.uu.se wrote: To clarify: the -hbn output is not very indicative of how many contacts there were since some of them could be present in one frame but absent in 99. The -num option, however, provides the number of contacts over time, and its time average probably tells you much more in this case. What version of g_hbond are you using? I remember there were several bugfixes over the last 6 months or so. With the latest version(s) I believe that the -merge flag has no effect on contact analysis, which is correct. Erik -- 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_hbond and contact
Thank you Sir. On Tue, Mar 5, 2013 at 4:33 PM, Erik Marklund er...@xray.bmc.uu.se wrote: On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote: Sir, I used gromacs 4.6. I got the point - index file will tell how many contacts an atom has made during the trajectory. Whether it has made a contact with an atom only in once or all the time, in the whole trajectory, it will be mentioned. Am I right? Yes. So from the problem I had, can I say that no. of contact/atom had increased in S2 while the no. of contact/time decreased? That depends. If 'contact' means unique interactions and 'atom' means e.g. all atoms in in your system, then yes. Its a bit confusing though! Thank you kavya On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund er...@xray.bmc.uu.se wrote: To clarify: the -hbn output is not very indicative of how many contacts there were since some of them could be present in one frame but absent in 99. The -num option, however, provides the number of contacts over time, and its time average probably tells you much more in this case. What version of g_hbond are you using? I remember there were several bugfixes over the last 6 months or so. With the latest version(s) I believe that the -merge flag has no effect on contact analysis, which is correct. Erik -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://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] g_hbond and contact
Dear users, I used the following tool for finding the contacts g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx -num a.xvg From the index file, the number of contacts of each atom was extracted. This and the xvg output was compared with another simulation. It was found that the number of contacts was more in 2nd simulation compared to the first. But When I compared xvg file it was showing the opposite behaviour. The contacts was also calculated using g_mdmat for the same cutoff and it was agreeing with the numbers I got from in index output of g_hbond. Why is this difference in index and xvg output? Also the xvg file looks like - s0 legend Contacts @ s1 legend Pairs within 0.4 nm 40007496 0 40027513 0 40047605 0 40067531 0 40087573 0 40107546 0 40127544 0 40147526 0 40167530 0 40187496 0 40207526 0 .. Thank you kavya -- 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_hbond and contact
Sir, From Index file which gives the unique contacts - First section the list of atoms I want to analyse [ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ] second section : the unique contacts of each atoms with others [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. I hope I am clear this time. Thank you kavya On Mon, Mar 4, 2013 at 10:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 11:25 AM, Kavyashree M wrote: Dear users, I used the following tool for finding the contacts g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx -num a.xvg From the index file, the number of contacts of each atom was extracted. This and the xvg output was compared with another simulation. It was found that the number of contacts was more in 2nd simulation compared to the first. But When I compared xvg file it was showing the opposite behaviour. These statements don't make any sense. How did you determine that the number of contacts in simulation 2 was greater than simulation 1, but then the .xvg files showed the opposite? The number of contacts come from the .xvg files? Perhaps you simply swapped your files during analysis. The contacts was also calculated using g_mdmat for the same cutoff and it was agreeing with the numbers I got from in index output of g_hbond. Why is this difference in index and xvg output? An index group is a list of atom numbers. The .xvg output is whatever you tell it to be, in this case, the number of contacts within the group selected. -Justin Also the xvg file looks like - s0 legend Contacts @ s1 legend Pairs within 0.4 nm 40007496 0 40027513 0 40047605 0 40067531 0 40087573 0 40107546 0 40127544 0 40147526 0 40167530 0 40187496 0 40207526 0 .. Thank you kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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_hbond and contact
On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote: When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. I gave a group of hydrophobic atoms in both cases The command I gave - g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx -r 0.4 -hbm o.xpm -hbn o.ndx -num o.xvg my index file contained a group of hydrophobic atoms. which I supplied in the x.ndx. You don't define contacts in an index group, you define atoms that may or may not make contacts with others. The one I mentioned here is the output index file from the g_hbond (4.6 version) - o.ndx. [ contacts_C_CA_CB_CD_CD1_CD2_**CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_**CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. I did not generate this. The tool (g_hbond) generated this index file. It is the -hbn output. From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. Thank you kavya -- 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_hbond and contact
I am sorry There is no 7ws Its a typographic error. What I wanted to ask was - I am comparing two simulations S1 and S2 for contacts at a given cut off I used g_mdmat and g_hbond to calculate it. g_hbond outputs: of -num and -hbn was considered. 1. -hbn output was analysed to calculate how many contacts each atom has from both S1 and S2. 2. -num output graph was compared from both S1 and S2. g_mdmat output: of -no was considered. 3. -no output was analysed from both S1 and S2 using the third column or the second Y value which gives total contacts of each atom. It was observed that 1 and 3 matched exactly giving the same number of contacts each atom has (in the whole simulations). indicating that the number of contacts each atom has was more in S2 than S1. But the graph from 2 indicated that the number of contacts (along the trajectory) in S1 was higher than S2. My doubt is: The number of contact per atom follows S2 S1 while number of contacts per time follows S1 S2. I am unclear as to what I have to conclude from this observations. - I used the same cutoff throughout. - There has not been any swapping of the trajectory while analysing. Thank you Kavya On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 1:10 PM, Kavyashree M wrote: On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote: When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. I gave a group of hydrophobic atoms in both cases The command I gave - g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx -r 0.4 -hbm o.xpm -hbn o.ndx -num o.xvg my index file contained a group of hydrophobic atoms. which I supplied in the x.ndx. You don't define contacts in an index group, you define atoms that may or may not make contacts with others. The one I mentioned here is the output index file from the g_hbond (4.6 version) - o.ndx. [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_*** *CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. I did not generate this. The tool (g_hbond) generated this index file. It is the -hbn output. OK, then I still don't know what 7ws is, but the only purpose for this file is to provide a key to the existence matrix in hbmap.xpm. Your previous description indicated that you were using it for some other analysis, which would not be appropriate. The other thing worth mentioning here is something that was posted to the list just a few hours ago, that the output of g_hbond -contact may not agree with other methods of calculating contacts, especially in the case of -merge vs. -nomerge. -Justin From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. Thank you kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use
[gmx-users] order in index and matrix
Dear users, I just wanted a small clarification whether the order of elements in matrix (-hbm) corresponds to reverse order of elements in the index file (-hbn) obtained from g_hbond? Thank you Kavya -- 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] Number of interactions per residue
Dear users, How can I get the number of interactions of each residue within a cut off as a function of time. just like g_saltbr writes with the option -sep. I tried using g_mdmat but it gives an average contact map. Thank you Kavya -- 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 interactions per residue
Thank you! On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Perhaps g_hbond -contact will do what you want. Erik On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote: Dear users, How can I get the number of interactions of each residue within a cut off as a function of time. just like g_saltbr writes with the option -sep. I tried using g_mdmat but it gives an average contact map. Thank you Kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://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] Re: Salt-bridge segmentation fault
Dear users, After simulation dimers appear separated, I was able to do saltbridge calculation on this. This will be different than doing it on a dimer which are together. Am I correct? Please reply.. Thank you Kavya On Thu, Feb 7, 2013 at 3:39 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, While calculating salt bridges using g_saltbr I got segmentation fault when I used trajectory with only the protein. But when I used the trajectory with water It worked. But the problem was that the monomers were far apart in the trajectory with water and not with the only-protein trajectory. Kindly help! Thank you Kavya -- 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: Regarding mean square displacement
Dear Sir, Thank you for the reply, It does not cross the boundary. I made the trajectory so that the dimers are together. I again calculated on a superposed trajectory, Then I got MSDs in the range of 0.01 to 0.15nm^2. But this is still higher than the value mentioned in the paper or is this acceptable? Thank you Kavya On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/6/13 11:49 PM, Kavyashree M wrote: Dear users, Since I am getting the mean square displacements in terms of several nm^2. I doubt it is wrong. Could anyone please explain me the solution for this. I checked the structure it is not denatured, In addition I used -rmcomm in order to remove the COM movements. Sounds like a PBC issue. Does your dimer split across periodic boundaries? If it does, then your MSD is going to go through the roof because it's measuring the MSD of the whole protein. -Justin On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I have a very basic question in MSD calculation. g_msd calculation on a protein dimer (~237 aa each) trajectory gave a plot of msd, with the values ranging between 1 to 14nm^2. But is this a sensible MSD? As the values given in a paper i was referring was in Ang^2 J. Chem. Theory Comput. 2012, 8, 1129-1142 Command that i used - echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000 -e 5 -rmcomm Is the range of diffusion coefficient of proteins of in water l in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s) Thank you kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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: Regarding mean square displacement
Dear Sir, Yes it is the same protein. Initially I had not superposed the structures in the trajectory. But this time I calculated the msd on a superposed trajectory (of the same simulation). the simulation is carried out on a dimer for 50ns using OPLS-AA and TIP4P water model. Using Gromacs4.5.3. If any other information is required Please let me know. Thank you Kavya On Thu, Feb 7, 2013 at 5:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/7/13 6:49 AM, Kavyashree M wrote: Dear Sir, Thank you for the reply, It does not cross the boundary. I made the trajectory so that the dimers are together. I again calculated on a superposed trajectory, Then I got MSDs in the range of 0.01 to 0.15nm^2. But this is still higher than the value mentioned in the paper or is this acceptable? Are you studying the same protein? Given sparse detail in an email thread, not knowing whether the simulations were done correctly or for sufficient time, no one can assess correctness here. -Justin On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/6/13 11:49 PM, Kavyashree M wrote: Dear users, Since I am getting the mean square displacements in terms of several nm^2. I doubt it is wrong. Could anyone please explain me the solution for this. I checked the structure it is not denatured, In addition I used -rmcomm in order to remove the COM movements. Sounds like a PBC issue. Does your dimer split across periodic boundaries? If it does, then your MSD is going to go through the roof because it's measuring the MSD of the whole protein. -Justin On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I have a very basic question in MSD calculation. g_msd calculation on a protein dimer (~237 aa each) trajectory gave a plot of msd, with the values ranging between 1 to 14nm^2. But is this a sensible MSD? As the values given in a paper i was referring was in Ang^2 J. Chem. Theory Comput. 2012, 8, 1129-1142 Command that i used - echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000 -e 5 -rmcomm Is the range of diffusion coefficient of proteins of in water l in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s) Thank you kavya -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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: Salt-bridge segmentation fault
Thank you, I have noticed this in the output of the g_saltbr. Later I separated the files according to what ever I require. My worry was only that of the dimeric interface which could not be seen because it is separated. I will try by giving a separate tpr file without water. Thank you Kavya On Thu, Feb 7, 2013 at 5:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/7/13 6:42 AM, Kavyashree M wrote: Dear users, After simulation dimers appear separated, I was able to do saltbridge calculation on this. This will be different than doing it on a dimer which are together. Am I correct? Most Gromacs tools handle PBC well for simple metrics like measurements. I would suspect that the seg fault comes from a mismatch in the .tpr and .xtc contents. g_saltbr is a rather stupid tool that tries to guess salt bridges based on anything that's charged, which includes ions and other groups that don't necessarily participate in such interactions (see the discussion on this same topic in recent days). Perhaps if g_saltbr is identifying elements that it wants to examine from the .tpr file but can't find them in the trajectory, you get a seg fault. This shouldn't happen, but you can also use tpbconv to produce a subset .tpr file with just the protein for the purposes of analysis. -Justin On Thu, Feb 7, 2013 at 3:39 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, While calculating salt bridges using g_saltbr I got segmentation fault when I used trajectory with only the protein. But when I used the trajectory with water It worked. But the problem was that the monomers were far apart in the trajectory with water and not with the only-protein trajectory. Kindly help! Thank you Kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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: Regarding mean square displacement
Thank you, My intention is mainly to compare the MSDs of the trajectory and not the diffusion as such. The paper I mentioned have used a tetramer for the similar analysis. Hence I wanted to know whether the values I obtained is sensible. Thank you Kavya On Thu, Feb 7, 2013 at 7:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/7/13 7:08 AM, Kavyashree M wrote: Dear Sir, Yes it is the same protein. Initially I had not superposed the structures in the trajectory. But this time I calculated the msd on a superposed trajectory (of the same simulation). the simulation is carried out on a dimer for 50ns using OPLS-AA and TIP4P water model. Using Gromacs4.5.3. If any other information is required Please let me know. The specific suitability of a protocol is dependent upon what you believe to be correct for your system based on precedent and chemical knowledge. Also be aware that post-processing of the trajectory to superimpose frames defeats the purpose of measuring diffusion - if you re-center or superimpose your structures, it's not diffusing! Dealing with a dimeric protein may be a challenge for which g_msd wasn't designed, so I don't know if there's an easy solution here. Perhaps someone else can suggest something. -Justin Thank you Kavya On Thu, Feb 7, 2013 at 5:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/7/13 6:49 AM, Kavyashree M wrote: Dear Sir, Thank you for the reply, It does not cross the boundary. I made the trajectory so that the dimers are together. I again calculated on a superposed trajectory, Then I got MSDs in the range of 0.01 to 0.15nm^2. But this is still higher than the value mentioned in the paper or is this acceptable? Are you studying the same protein? Given sparse detail in an email thread, not knowing whether the simulations were done correctly or for sufficient time, no one can assess correctness here. -Justin On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/6/13 11:49 PM, Kavyashree M wrote: Dear users, Since I am getting the mean square displacements in terms of several nm^2. I doubt it is wrong. Could anyone please explain me the solution for this. I checked the structure it is not denatured, In addition I used -rmcomm in order to remove the COM movements. Sounds like a PBC issue. Does your dimer split across periodic boundaries? If it does, then your MSD is going to go through the roof because it's measuring the MSD of the whole protein. -Justin On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I have a very basic question in MSD calculation. g_msd calculation on a protein dimer (~237 aa each) trajectory gave a plot of msd, with the values ranging between 1 to 14nm^2. But is this a sensible MSD? As the values given in a paper i was referring was in Ang^2 J. Chem. Theory Comput. 2012, 8, 1129-1142 Command that i used - echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000 -e 5 -rmcomm Is the range of diffusion coefficient of proteins of in water l in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s) Thank you kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin** http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.**biochem.vt.**edu/Pages/**Personal/justin http://www.**bevanlab.biochem.vt.edu/Pages/**Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search**h**ttp://www.gromacs.org/**Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/**Support
[gmx-users] Regarding mean square displacement
Dear users, I have a very basic question in MSD calculation. g_msd calculation on a protein dimer (~237 aa each) trajectory gave a plot of msd, with the values ranging between 1 to 14nm^2. But is this a sensible MSD? As the values given in a paper i was referring was in Ang^2 J. Chem. Theory Comput. 2012, 8, 1129-1142 Command that i used - echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000 -e 5 -rmcomm Is the range of diffusion coefficient of proteins of in water l in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s) Thank you kavya -- 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: Regarding mean square displacement
Dear users, Since I am getting the mean square displacements in terms of several nm^2. I doubt it is wrong. Could anyone please explain me the solution for this. I checked the structure it is not denatured, In addition I used -rmcomm in order to remove the COM movements. Kindly reply Thank you Kavya On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I have a very basic question in MSD calculation. g_msd calculation on a protein dimer (~237 aa each) trajectory gave a plot of msd, with the values ranging between 1 to 14nm^2. But is this a sensible MSD? As the values given in a paper i was referring was in Ang^2 J. Chem. Theory Comput. 2012, 8, 1129-1142 Command that i used - echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000 -e 5 -rmcomm Is the range of diffusion coefficient of proteins of in water l in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s) Thank you kavya -- 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] Superimposed trajectory
Thank you Sir! Kavya On Thu, Feb 7, 2013 at 11:18 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: trjconv -fit rot+trans Cheers, Tsjerk On Thu, Feb 7, 2013 at 6:19 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Which tool can be used to create a trajectory of structures (from each frame) superimposed on the first frame using the original traj.xtc file? Thank you kavya -- 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. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] Re: clarification regarding contact map - g_mdmat
Dear users, Sorry. It is because the unit of the cutoff distance ]is in nm. Thank you kavya On Fri, Feb 1, 2013 at 1:28 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I used g_mdmap to calculate the C-alpha contact map of the trajectory. the distance cut off of 8.0 Ang was selected The protein is a dimer of 237 residues. The output of -no was like this - #resratio tot mean natm mean/atm 1 1.000 473 473.0001 473.000 2 1.000 473 473.0001 473.000 3 1.000 473 473.0001 473.000 4 1.000 473 473.0001 473.000 5 1.000 473 473.0001 473.000 6 1.000 473 473.0001 473.000 7 1.000 473 473.0001 473.000 So it mean that on an average each calpha atom contacts all other C-alpha atom in the whole trajectory at some point of time. In order to cross check it I collected data only for one time frame. This was also very similar results. all the residues have a minimum of atleast 471 contacts. Some one kindly clarify where I am going wrong.? the command I used was - g_mdmat -f .*.xtc -s *.tpr -no *.xvg -mean *.xpm -b 4000 -e 4000 -t 8.0 Is this trucating distance in Angstroms or nanometer? Thank you Kavya -- 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] clarification regarding contact map - g_mdmat
Dear users, I used g_mdmap to calculate the C-alpha contact map of the trajectory. the distance cut off of 8.0 Ang was selected The protein is a dimer of 237 residues. The output of -no was like this - #resratio tot mean natm mean/atm 1 1.000 473 473.0001 473.000 2 1.000 473 473.0001 473.000 3 1.000 473 473.0001 473.000 4 1.000 473 473.0001 473.000 5 1.000 473 473.0001 473.000 6 1.000 473 473.0001 473.000 7 1.000 473 473.0001 473.000 So it mean that on an average each calpha atom contacts all other C-alpha atom in the whole trajectory at some point of time. In order to cross check it I collected data only for one time frame. This was also very similar results. all the residues have a minimum of atleast 471 contacts. Some one kindly clarify where I am going wrong.? the command I used was - g_mdmat -f .*.xtc -s *.tpr -no *.xvg -mean *.xpm -b 4000 -e 4000 -t 8.0 Is this trucating distance in Angstroms or nanometer? Thank you Kavya -- 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 matrix of the trajectory
Dear users, While calculating the distance matrix using g_mdmat, with -no option, it gives an xvg output pertaining the total, mean etc contacts of the residue within 1.5Ang in the trajectory. I calculated the same for a single frame (or pdb file) #resratio tot mean natm mean/atm 1 1.000 640 640.000 1933.684 2 1.000 530 530.000 1731.176 3 1.000 805 805.000 2236.591 4 1.000 571 571.000 1733.588 I am little doubtful about the number under total. Does this mean that the atoms of that residue has total of 640 contacts (in one frame)? Are there any otherway to get contact map for the whole trajectory where we can mention min and max cut-off distance? Thank you kavya -- 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] Hydrogen bonding differences
Dear Sir, Sure I will try with 4.6. presently I am not able to download it. Thank you kavya On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There were a handful of bugfixes to g_hbond over the last year. Could you try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form before. Erik On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote: Dear Sir, This is 4.5.3. I have not tried nomerge. I did not use nomerge option in any of them, So if it has counted it (Hbond b/w same donor and acceptor but with different hydrogen) twice in one calculation then it will be counted twice in another, So wont the result with/without nomerge be the same? The difference is 4-5 Hbonds.. Thank you Kavya On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi. What version was this? Have you tried with -nomerge? Erik On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: Dear users, While calculating hydrogen bonds for a simulation, it was found that the average number of intra protein hbonds was not equal to sum of MM, MS and SS hydrogen bonds. (MM - main chain - main chain, MS - main chain - side chain and side chain - side chain hydrogen bonds). There was a difference of 5 or so hbonds between intra-protein and MM+MS+SS hbonds. why is this so? I selected the options 7 7 for MM, 7 8 for MS and 8 8 for SS hydrogen bonds. One clarification. nhbdist option gives 0, 1, 2, 3 and total hydrogen bonds per hydrogen. Does this mean that a single hydrogen involving in forming hbond with 2 different acceptors/donors at different points of time in the trajectory. Thanks kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://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] Hydrogen bonding differences
Dear Sir, This is 4.5.3. I have not tried nomerge. I did not use nomerge option in any of them, So if it has counted it (Hbond b/w same donor and acceptor but with different hydrogen) twice in one calculation then it will be counted twice in another, So wont the result with/without nomerge be the same? The difference is 4-5 Hbonds.. Thank you Kavya On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi. What version was this? Have you tried with -nomerge? Erik On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: Dear users, While calculating hydrogen bonds for a simulation, it was found that the average number of intra protein hbonds was not equal to sum of MM, MS and SS hydrogen bonds. (MM - main chain - main chain, MS - main chain - side chain and side chain - side chain hydrogen bonds). There was a difference of 5 or so hbonds between intra-protein and MM+MS+SS hbonds. why is this so? I selected the options 7 7 for MM, 7 8 for MS and 8 8 for SS hydrogen bonds. One clarification. nhbdist option gives 0, 1, 2, 3 and total hydrogen bonds per hydrogen. Does this mean that a single hydrogen involving in forming hbond with 2 different acceptors/donors at different points of time in the trajectory. Thanks kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://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] g_hbond existence matrix
Dear users, I have a little confusion - The hbmap.xpm file gives the existence of each hydrogen bond. The file mentions - c #FF /* None */, o c #FF /* Present */, Meaning - character space in white colour means Hbond not present character o in red colour means Hbond is present. In addition, the file also contains white coloured o what is this? Thank you Kavya -- 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_hbond existence matrix
Thank you for the clarification. On Fri, Jan 25, 2013 at 12:40 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/24/13 11:03 AM, Kavyashree M wrote: Dear users, I have a little confusion - The hbmap.xpm file gives the existence of each hydrogen bond. The file mentions - c #FF /* None */, o c #FF /* Present */, Meaning - character space in white colour means Hbond not present character o in red colour means Hbond is present. In addition, the file also contains white coloured o what is this? There are only two characters in the .xpm file, a space and an 'o' as you noted above. The font color that appears in your terminal is whatever you have set it to be; there is no significance of different colored letters in the .xpm file. There either is a hydrogen bond in a frame (in which case you see 'o') or there is not (and thus a blank space). -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] g_saltbr not include side chains of GLU and ASP??
Dear users, I used g_saltbr to calculate the salt-bridge interactions using: g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep It gave the output for each atom-atom interaction within the given cut-off. When I checked the atom type that corresponds to the atom number output in each file, side chain oxygen atoms of ASP and GLU was not present in any of the file. And most of the atoms that corresponds to the ASP and GLU were CB, CG or CD. Kindly someone clarify why is this so. Thank you Kavya -- 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: g_saltbr not include side chains of GLU and ASP??
Dear users, I would like to add that in case of ARG or LYS, the sidechain nitrogen atoms (NE,NZ,NH1,NH2) are present in the output. The problem s only with GLU and ASP residues. I use 4.5.3 version Thank you kavya On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I used g_saltbr to calculate the salt-bridge interactions using: g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep It gave the output for each atom-atom interaction within the given cut-off. When I checked the atom type that corresponds to the atom number output in each file, side chain oxygen atoms of ASP and GLU was not present in any of the file. And most of the atoms that corresponds to the ASP and GLU were CB, CG or CD. Kindly someone clarify why is this so. Thank you Kavya -- 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: g_saltbr not include side chains of GLU and ASP??
Sir, I used OPLS-AA ff. Thank you very mush for your effort. Its clear now. AS you said It assigns the number of the 1st atom of the charge group in the output file. Thank you kavya On Thu, Jan 3, 2013 at 5:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/3/13 5:15 AM, Kavyashree M wrote: Dear users, I would like to add that in case of ARG or LYS, the sidechain nitrogen atoms (NE,NZ,NH1,NH2) are present in the output. The problem s only with GLU and ASP residues. I use 4.5.3 version I only took a quick look through the code, but it seems that what g_saltbr is doing is labeling its output files based on the first atom in a given charge group. The charge group, not the individual atoms per se, are what dictate the search criteria. You haven't said which force field you're using, but I will assume it's one of the Gromos ones, wherein the C[GD] atom is the first atom in the COO- charge group. -Justin Thank you kavya On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I used g_saltbr to calculate the salt-bridge interactions using: g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep It gave the output for each atom-atom interaction within the given cut-off. When I checked the atom type that corresponds to the atom number output in each file, side chain oxygen atoms of ASP and GLU was not present in any of the file. And most of the atoms that corresponds to the ASP and GLU were CB, CG or CD. Kindly someone clarify why is this so. Thank you Kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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_dih calculation doubt
Thanks both of you for the suggestions. Regarding the backup files - I did not run the command multiple times. Thank you kavya On Thu, Dec 27, 2012 at 1:01 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Unfortunately, g_dih was written before 1997 and its documentation is very poor. It does not actually read the connectivity in the .tpr file, nor does it attempt to infer connectivity other than for some protein backbone dihedrals. For some reason, it thinks it finds some for your topology, but can't find parameters for them (wherever it imagines it should find them). As far as I can see, its functionality is entirely duplicated by g_angle, so g_dih will probably be removed in 4.6. I suggest you use g_angle for whatever you are trying to do. Mark On Wed, Dec 26, 2012 at 4:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/26/12 12:57 AM, Kavyashree M wrote: Dear users, I was using g_dih to find the phi/psi transitions of a protein along the trajectory using the following command - g_dih -f a.xtc -s a.tpr -o dihout.out -b x -e y -w When it started running it indicated many of the following lines Dihedral around 7793,7804 not found in topology. Using mult=3 what does it mean..? they are not nearby atoms so as to calculate dihedral angle.. Clearly g_dih thinks they are. Refer to your coordinate or topology files to find out what those atoms are. A difference of only 11 atoms is not very large. They could indeed be in the same residue or in a disulfide. At the end it gave the dihedral transitions of each residue along the trajectory - it displayed - Calculated all dihedrals, now analysing... and then it took backup of all residue transitions creating new xvg files of the same residues. I compared the two files ie, the backup file and the corresponding new file there was drastic differences why is there difference between these two files although both are plots of degrees v/s time. Backup files are generated after multiple invocations of a command. Apparently whatever you ran multiple times produced different output. One more question is some times it shows dihedral values of more than 360.. sometimes 1000 etc.. does it mean that the bond has undergone rotation so many times.. I am sorry I am not getting this. Also the file that it generates does not say which is phi/psi specifically. So I suppose 2nd column is phi and 3rd column is psi? it it right? You'll have to provide snippets of your output, with complete .xvg header information here. Most files are very well labeled so as to make the columns obvious. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 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
Re: [gmx-users] g_hbond index
Sir, I thought that the order should not matter but when I used 18 - 1 and 1 - 18 the graph were slightly off. Group 18 is a set of residues in that protein with some unique property. I wanted to see the variation of Hbond of these residues with the whole protein. so group 18 is a subset of group 1. Thank you Kavya On Wed, Dec 19, 2012 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/19/12 9:37 AM, Kavyashree M wrote: Dear users, While using g_hbond, does it make any difference if I give option 18 and 1 or 1 and 18? Order does not matter. I wanted to find the hydrogen bonding of a group of residues with the whole protein so I had an index of this group. When I give the option as 18 (index number) and 1 (whole protein), I get several messages Hm. This isn't the first time I found this donor (...,...) But later it does calculates. does this mean that it is double counting those interactions? What is group 18? Be mindful of the g_hbond requirement that the chosen groups must be completely unique or completely overlapping. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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_hbond index
Ok thank you. kavya On Wed, Dec 19, 2012 at 10:52 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/19/12 11:43 AM, Kavyashree M wrote: Sir, I thought that the order should not matter but when I used 18 - 1 and 1 - 18 the graph were slightly off. Group 18 is a set of residues in that protein with some unique property. I wanted to see the variation of Hbond of these residues with the whole protein. so group 18 is a subset of group 1. You see a difference likely because you are invoking the command incorrectly (with overlapping index groups) and it is affecting the way the donor and acceptor arrays are constructed. The proper method of analysis is to monitor H-bonds within group 18 and then between group 18 and whatever part of the protein that does not overlap with it. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Re: g_sas : Total surface area
Dear users, Am I clear with the question? Thank you Kavya On Wed, Dec 12, 2012 at 1:36 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I was calculating solvent accessible surface area for a trajectory using g_sas. I used an index file with 3 sets (A, B, C) of mutually exclusive residues but summing up to 20 amino acids. Then using g_sas calculated sas for these 3 sets separately and whole protein separately for the same trajectory. I was expecting that the average value of Total surface area (protein) ~ Total surface area (A)+Total surface area (B)+Total surface area (C) But it is not so. Could anyone explain me why? Thank you Kavya -- 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: g_sas : Total surface area
Dear users, Anything wrong in my question? Kindly give some suggestions. Thank you Kavya On Wed, Dec 12, 2012 at 3:23 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Am I clear with the question? Thank you Kavya On Wed, Dec 12, 2012 at 1:36 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I was calculating solvent accessible surface area for a trajectory using g_sas. I used an index file with 3 sets (A, B, C) of mutually exclusive residues but summing up to 20 amino acids. Then using g_sas calculated sas for these 3 sets separately and whole protein separately for the same trajectory. I was expecting that the average value of Total surface area (protein) ~ Total surface area (A)+Total surface area (B)+Total surface area (C) But it is not so. Could anyone explain me why? Thank you Kavya -- 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_sas : Total surface area
Thank you very much for your replies. The system consists of a homodimer in tip4p dodecahedron box simulated using OPLSAA ff. The A B C here are the amino acids: A- S T N Q G P H B- A V L I M C F Y W C- D E K R So these are set in an index file and i used each one of these to calculate sasa in g_sas. When the g_sas calculation starts it specifies the number of hydrophobic atoms, one of the example - For the whole protein - 4644 out of 7590 atoms were classified as hydrophobic For group A of same protein - 702 out of 1424 atoms were classified as hydrophobic For group B of same protein - 2614 out of 3496 atoms were classified as hydrophobic For group C of same protein - 1328 out of 2670 atoms were classified as hydrophobic In this the number of hydrophobic atoms of A, B and C adds up to the total hydrophobic atoms in whole protein. but after the calculation is over the average values of Total sas (legend S2 of area.xvg file) of the protein and Total sas of A, B and C are given below Whole protein - 254.04nm^(-2) A - 175.87nm^(-2) B - 211.33nm^(-2) C - 264.65nm^(-2) I expected that the average total sas of Whole protein atleast approximately equal the sum of Total sas of A, B and C. If not why? All calculations are done for the same trajectory after equilibrating. Thank you Kavya On Wed, Dec 12, 2012 at 5:20 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi Kavya, Can you better describe your system? As Mark suggested, could you supply some number? Francesco 2012/12/12 Mark Abraham mark.j.abra...@gmail.com On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I was calculating solvent accessible surface area for a trajectory using g_sas. I used an index file with 3 sets (A, B, C) of mutually exclusive residues but summing up to 20 amino acids. Then using g_sas calculated sas for these 3 sets separately and whole protein separately for the same trajectory. I was expecting that the average value of Total surface area (protein) ~ Total surface area (A)+Total surface area (B)+Total surface area (C) But it is not so. Could anyone explain me why? Not without seeing any numbers. You're probably thinking that the surface area of A excludes the interfacial area to the other sets, but it doesn't. Mark -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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_sas : Total surface area
Sir, Oh! I was using sunset index numbers for both. I am sorry. I will try that and see. First option as protein and next the subset. Thank you very much. Kavya On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/12/12 9:37 AM, Kavyashree M wrote: Thank you very much for your replies. The system consists of a homodimer in tip4p dodecahedron box simulated using OPLSAA ff. The A B C here are the amino acids: A- S T N Q G P H B- A V L I M C F Y W C- D E K R So these are set in an index file and i used each one of these to calculate sasa in g_sas. When the g_sas calculation starts it specifies the number of hydrophobic atoms, one of the example - For the whole protein - 4644 out of 7590 atoms were classified as hydrophobic For group A of same protein - 702 out of 1424 atoms were classified as hydrophobic For group B of same protein - 2614 out of 3496 atoms were classified as hydrophobic For group C of same protein - 1328 out of 2670 atoms were classified as hydrophobic In this the number of hydrophobic atoms of A, B and C adds up to the total hydrophobic atoms in whole protein. but after the calculation is over the average values of Total sas (legend S2 of area.xvg file) of the protein and Total sas of A, B and C are given below Whole protein - 254.04nm^(-2) A - 175.87nm^(-2) B - 211.33nm^(-2) C - 264.65nm^(-2) I expected that the average total sas of Whole protein atleast approximately equal the sum of Total sas of A, B and C. If not why? All calculations are done for the same trajectory after equilibrating. Are you selecting the correct groups when running g_sas? For instance, you should be selecting Protein for the surface calculation, and then your custom subsets for output. If you use the subsets for both surface calculation and output, you will get an artificially inflated value that includes extra surface area that is actually buried in the context of the whole structure. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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_sas : Total surface area
I meant subset :) On Wed, Dec 12, 2012 at 8:21 PM, Kavyashree M hmkv...@gmail.com wrote: Sir, Oh! I was using sunset index numbers for both. I am sorry. I will try that and see. First option as protein and next the subset. Thank you very much. Kavya On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/12/12 9:37 AM, Kavyashree M wrote: Thank you very much for your replies. The system consists of a homodimer in tip4p dodecahedron box simulated using OPLSAA ff. The A B C here are the amino acids: A- S T N Q G P H B- A V L I M C F Y W C- D E K R So these are set in an index file and i used each one of these to calculate sasa in g_sas. When the g_sas calculation starts it specifies the number of hydrophobic atoms, one of the example - For the whole protein - 4644 out of 7590 atoms were classified as hydrophobic For group A of same protein - 702 out of 1424 atoms were classified as hydrophobic For group B of same protein - 2614 out of 3496 atoms were classified as hydrophobic For group C of same protein - 1328 out of 2670 atoms were classified as hydrophobic In this the number of hydrophobic atoms of A, B and C adds up to the total hydrophobic atoms in whole protein. but after the calculation is over the average values of Total sas (legend S2 of area.xvg file) of the protein and Total sas of A, B and C are given below Whole protein - 254.04nm^(-2) A - 175.87nm^(-2) B - 211.33nm^(-2) C - 264.65nm^(-2) I expected that the average total sas of Whole protein atleast approximately equal the sum of Total sas of A, B and C. If not why? All calculations are done for the same trajectory after equilibrating. Are you selecting the correct groups when running g_sas? For instance, you should be selecting Protein for the surface calculation, and then your custom subsets for output. If you use the subsets for both surface calculation and output, you will get an artificially inflated value that includes extra surface area that is actually buried in the context of the whole structure. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Asymmetry in homo dimer simulation
Sir, I also have come across several papers where they have done single simulations but in recent days most of them perform multiple trajectories for shorter period. But I am not clear how can multiple trajectories for shorter period of time compensate for single extended time simulation. Thank you Kavya On Thu, Dec 6, 2012 at 3:56 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 5 dec 2012 kl. 17.26 skrev Justin Lemkul: On 12/5/12 11:21 AM, Kavyashree M wrote: Sir, Thank you for your suggestions. I decided the cutoff based on RMSD convergence. I will calculate at different time intervals. Running multiple simulation is definitely the best suggestion but due to time and machine constraint it would be difficult. Instead I have two mesophilic simulations. But Is there any other way by which I can prove this point? Not using single trajectories. Your job is to convince reviewers that your work is sound. A single trajectory is not convincing, at least to any reviewer that does his or her homework :) I don't think that the use of single trajectories is necessarily wrong, as long as they are sufficiently long. It's usually the amount of sampling that is the crucial point, no? Erik -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Asymmetry in homo dimer simulation
Sir, Thank you for the reply. Total simulated time is 50ns. first 4ns is left and only 4-50ns were considered for rmsf calculations. T1 is 300K and T2 is 363K the protein being simulated is from Ecoli (mesophilic). As you have mentioned I do not have replicates of simulations hence only one 50ns simulation per temperature. And this happened in two proteins that I had simulated both are form mesophilic origin. Thank you Kavya On Wed, Dec 5, 2012 at 9:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/5/12 10:56 AM, Kavyashree M wrote: Dear users, I have simulated a homodimer (both the chains with same number of amino acids and in same configuration) using gromacs 453 in OPLSAA force field at 2 different temperatures (say T1 and T2). It was noticed that the rms fluctuation of chain A differs from chain B in both the simulations. In one of the temperature (T2) the rmsf of the protein is supposed to be more compared to the other (T1). When I compare rmsf of chain A at T1 with chain A at T2 (similarly for chain B). I observed that it shows opposite behaviour. ie chainB is having increased fluctuation at T1 than at T2. But actually i observed that the fluctuation of chain A at T1 resembles the fluctuation of chain B at T2 (with increased values) and similarly the fluctuations of chain B at T1 resembles that of chain A fluctuation at T2 (with increased values). Is this possible? or is there anything wrong? Your results would indicate simply that while one protein subunit fluctuates more, the other becomes somewhat more rigid. That's plausible, but perhaps not intuitive. Keep in mind that RMSF is very sensitive to whether or not your simulations are actually converged, and a single trajectory under each condition is insufficient to make very solid claims about anything. How long are the simulations? How much of the initial time is being disregarded, and thus how long are the equilibrated segments of the simulations? How different are T1 and T2? -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Asymmetry in homo dimer simulation
Dear users, One more question is. Is there a way to prove my point? Thank you Kavya On Wed, Dec 5, 2012 at 9:43 PM, Kavyashree M hmkv...@gmail.com wrote: Sir, Thank you for the reply. Total simulated time is 50ns. first 4ns is left and only 4-50ns were considered for rmsf calculations. T1 is 300K and T2 is 363K the protein being simulated is from Ecoli (mesophilic). As you have mentioned I do not have replicates of simulations hence only one 50ns simulation per temperature. And this happened in two proteins that I had simulated both are form mesophilic origin. Thank you Kavya On Wed, Dec 5, 2012 at 9:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/5/12 10:56 AM, Kavyashree M wrote: Dear users, I have simulated a homodimer (both the chains with same number of amino acids and in same configuration) using gromacs 453 in OPLSAA force field at 2 different temperatures (say T1 and T2). It was noticed that the rms fluctuation of chain A differs from chain B in both the simulations. In one of the temperature (T2) the rmsf of the protein is supposed to be more compared to the other (T1). When I compare rmsf of chain A at T1 with chain A at T2 (similarly for chain B). I observed that it shows opposite behaviour. ie chainB is having increased fluctuation at T1 than at T2. But actually i observed that the fluctuation of chain A at T1 resembles the fluctuation of chain B at T2 (with increased values) and similarly the fluctuations of chain B at T1 resembles that of chain A fluctuation at T2 (with increased values). Is this possible? or is there anything wrong? Your results would indicate simply that while one protein subunit fluctuates more, the other becomes somewhat more rigid. That's plausible, but perhaps not intuitive. Keep in mind that RMSF is very sensitive to whether or not your simulations are actually converged, and a single trajectory under each condition is insufficient to make very solid claims about anything. How long are the simulations? How much of the initial time is being disregarded, and thus how long are the equilibrated segments of the simulations? How different are T1 and T2? -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Asymmetry in homo dimer simulation
Sir, Thank you for your suggestions. I decided the cutoff based on RMSD convergence. I will calculate at different time intervals. Running multiple simulation is definitely the best suggestion but due to time and machine constraint it would be difficult. Instead I have two mesophilic simulations. But Is there any other way by which I can prove this point? Thank you Kavya On Wed, Dec 5, 2012 at 9:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/5/12 11:13 AM, Kavyashree M wrote: Sir, Thank you for the reply. Total simulated time is 50ns. first 4ns is left and only 4-50ns were considered for rmsf calculations. T1 is 300K and T2 is 363K the protein being simulated is from Ecoli (mesophilic). I would suggest you compare different, overlapping blocks of time as a further assessment of convergence. What motivated the choice of the 4-50 ns time frame? Simple RMSD stability? While that may be one way to assess convergence, it is not necessarily definitive. If you analyze your RMSF results over different times, i.e. 4-50, 10-50, 20-50, etc, how do they compare? As you have mentioned I do not have replicates of simulations hence only one 50ns simulation per temperature. I would encourage you to run more simulations. One trajectory is not definitive. -Justin And this happened in two proteins that I had simulated both are form mesophilic origin. Thank you Kavya On Wed, Dec 5, 2012 at 9:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/5/12 10:56 AM, Kavyashree M wrote: Dear users, I have simulated a homodimer (both the chains with same number of amino acids and in same configuration) using gromacs 453 in OPLSAA force field at 2 different temperatures (say T1 and T2). It was noticed that the rms fluctuation of chain A differs from chain B in both the simulations. In one of the temperature (T2) the rmsf of the protein is supposed to be more compared to the other (T1). When I compare rmsf of chain A at T1 with chain A at T2 (similarly for chain B). I observed that it shows opposite behaviour. ie chainB is having increased fluctuation at T1 than at T2. But actually i observed that the fluctuation of chain A at T1 resembles the fluctuation of chain B at T2 (with increased values) and similarly the fluctuations of chain B at T1 resembles that of chain A fluctuation at T2 (with increased values). Is this possible? or is there anything wrong? Your results would indicate simply that while one protein subunit fluctuates more, the other becomes somewhat more rigid. That's plausible, but perhaps not intuitive. Keep in mind that RMSF is very sensitive to whether or not your simulations are actually converged, and a single trajectory under each condition is insufficient to make very solid claims about anything. How long are the simulations? How much of the initial time is being disregarded, and thus how long are the equilibrated segments of the simulations? How different are T1 and T2? -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe
Re: [gmx-users] Asymmetry in homo dimer simulation
Sir, Oh! Thanks for good suggestion. Will find a way out. Kavya On Wed, Dec 5, 2012 at 9:56 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/5/12 11:21 AM, Kavyashree M wrote: Sir, Thank you for your suggestions. I decided the cutoff based on RMSD convergence. I will calculate at different time intervals. Running multiple simulation is definitely the best suggestion but due to time and machine constraint it would be difficult. Instead I have two mesophilic simulations. But Is there any other way by which I can prove this point? Not using single trajectories. Your job is to convince reviewers that your work is sound. A single trajectory is not convincing, at least to any reviewer that does his or her homework :) -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Dimer jumping during simulation
Dear users, I have simulated a protein dimer using OPLS-AA in 4.5.3 version. Analysing simulation showed that one of the monomer is out side the box. I tried trjconv pbc -nojump and trjconv -pbc mol still some fraction of a time one of them goes out. Can anyone suggest some solution to this. I need to calculate the radius of gyration of dimer, this value differs when i use treated and untreated trajectories. So Kindly suggest some solution. Thank you kavya -- 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: Dimer jumping during simulation
Dear users, I used -center along with -pbc mol selecting protein for both options Its fine now both monomers are in the box. Thanks kavya On Sun, Dec 2, 2012 at 1:47 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I have simulated a protein dimer using OPLS-AA in 4.5.3 version. Analysing simulation showed that one of the monomer is out side the box. I tried trjconv pbc -nojump and trjconv -pbc mol still some fraction of a time one of them goes out. Can anyone suggest some solution to this. I need to calculate the radius of gyration of dimer, this value differs when i use treated and untreated trajectories. So Kindly suggest some solution. Thank you kavya -- 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] problem in running md simulation
Hi Ananya, Can you try with rvwd 0.9nm and rcolumb with 1.4nm..? vdw interaction decreases as 1/r^6, while columbic interaction decreases as (1/r).. so it would be better if you consider columbic interaction for longer distance than vdw interaction.. bye kavya On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, As suggested by venhat I have energy minimised it till 1000Kj/mol but even now I am getting the same error, saying Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 90.674 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --**- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. can anyone suggest me what to do now. Ananya Chatterejee On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote: I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee ananyachatter...@iiserkol.ac.**in ananyachatter...@iiserkol.ac.in wrote: Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 226.610 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. kindly help me I am not getting where I am getting wrong. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- gmx-users mailing list
Re: [gmx-users] problem in running md simulation
Oh, I am sorry That is right. But its difficult to find The specific cutoff values to be used for different protocols of cutoff, switch and shift.. different values are stated in different papers.. And original force field paper (eg OPLSAA) does not explicitly specify these values. Any references regarding this will be helpful for the users. bye kavya On Fri, Nov 16, 2012 at 8:52 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/16/12 10:10 AM, Kavyashree M wrote: Hi Ananya, Can you try with rvwd 0.9nm and rcolumb with 1.4nm..? vdw interaction decreases as 1/r^6, while columbic interaction decreases as (1/r).. so it would be better if you consider columbic interaction for longer distance than vdw interaction.. One should not make haphazard changes to cutoffs. They are part of the force field. Changing them without basis can invalidate the force field model. -Justin bye kavya On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee ananyachatter...@iiserkol.ac.**in ananyachatter...@iiserkol.ac.in wrote: Hi all, As suggested by venhat I have energy minimised it till 1000Kj/mol but even now I am getting the same error, saying Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size t = 90.674 ps: Water molecule starting at atom 236548 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. can anyone suggest me what to do now. Ananya Chatterejee On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote: I think the system is not well energy minimized. Do it for 1000kj/mol. Also check for bad contacts in your starting structure using Ramachandran plot. One more important thing is that, you have to generate an index file with Protein_GTP as one group and water_Ions as another. Then change your tc-groups as tc-grps = Protein_GTP Water_Ions tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in ananyachatter...@iiserkol.ac.**inananyachatter...@iiserkol.ac.in wrote: Hi all, I was running a md simulation of protein complexed with GTP in water, neutralised with Mg2+ and Cl- ions.I have also em the system to 2000kj/mol and also equilibrated the water molecules in 300K temperature and 1 bar pressure. And then run the md simulation using md parameters as follow: title = Protein-ligand complex ; Run parameters integrator = md; leap-frog integrator nsteps = 50 ; 2 * 500 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1ps nstvout = 500 ; save coordinates every 1ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein GTP SOL MG2+ ; Bond parameters constraints = none; No constrains ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Temperature coupling tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = Protein GTP SOL MG2+ CL-; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 0.1 0.1 ; time constant, in ps ref_t = 300 300 300 300 300; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC Now I am getting the following error. Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding
Re: [gmx-users] how to restart a stopped simulation
Hi Ananya, You can refer this. http://www.gromacs.org/Documentation/How-tos/Doing_Restarts?highlight=restarting bye kavya On Mon, Nov 12, 2012 at 11:27 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hi all, my simulation has stopped due to power failure, can anyone tell me how to restart it from the same point. -- Ananya Chatterjee, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] how to check the intermediate coordinated even when the simulation is running
Hi ananya, You can get the coordinates using trjconv: trjconv -f file.xtc -s file.tpr -o file.pdb -b initial time in ps -e final time in ps this will give you pdb at the time you have mentioned. For your first question- as far as I know you need to check whether there is any periodic image violation using g_mindist. Other things what you have to check depends on the parameter you want to see. Probably others may give a better answer regarding this. Bye kavya On Fri, Nov 9, 2012 at 5:04 PM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: I am very new to this MD simulation, by reading the tutorials in the website I have run an simulation and it is running from last 5 day and I am not getting whether it is running properly or not. Could any one kindly tell me how to see whether the simulation is running or not and also how can I check the intermediate coordinated even when the simulation is running. Kindly help me. -- Ananya Chatterjee, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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_saltbr speed
Dear users, Its the continuation of the question I asked yesterday, Inorder to reduce the memory usage during g_saltbr calculations i got the trajectory of only protein, and tpr file without water and was able to successfully run it. But unfortunately this again got stopped at 36ns as it had stopped when i was using the whole trajectory. I tried with -dt 2, still the same problem exists. Kindly suggest a way out of this situation. Thank you With Regards Kavya On Thu, Jul 12, 2012 at 6:11 PM, Kavyashree M hmkv...@gmail.com wrote: Dear Sir, Thank you It worked :). a very usefull suggestion. But it did not promt to choose any option. I used index file. Thank you Kavya On Thu, Jul 12, 2012 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 8:31 AM, Kavyashree M wrote: Ok may be i need to specify an index file. I will try that. And regarding the WARNING: this .tpx file is not fully functional. I hope it will work fine enough to finish g_saltbr calculation? In principle, you should be prompted to choose a default group, but you can also use a custom index group as needed. The warning message is intended to note that the .tpr file you produce will not likely work for running an actual simulation. It should be fine for analysis. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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_saltbr speed
Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will that be insufficient? I have previously run other analysis which used to take huge memory, for eg. covariance analysis, in a system with much lesser memory even though CPU usage was low the job used to finish. But in this case its not so. Thank you kavya On Fri, Jul 13, 2012 at 9:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/13/12 11:50 AM, Kavyashree M wrote: Dear users, Its the continuation of the question I asked yesterday, Inorder to reduce the memory usage during g_saltbr calculations i got the trajectory of only protein, and tpr file without water and was able to successfully run it. But unfortunately this again got stopped at 36ns as it had stopped when i was using the whole trajectory. I tried with -dt 2, still the same problem exists. Kindly suggest a way out of this situation. How long is the trajectory? How many frames? What is the size of the file on disk? It sounds to me like you're simply exhausting available memory, so the only advice is in the link I posted before - use fewer frames or use a machine that has more memory to do the analysis. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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_saltbr speed
Ok... I will try other options. Thanks Kavya On Fri, Jul 13, 2012 at 10:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/13/12 12:05 PM, Kavyashree M wrote: Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will that be insufficient? I have previously run other analysis which used to take huge memory, for eg. covariance analysis, in a system with much lesser memory even though CPU usage was low the job used to finish. But in this case its not so. I can't see a reason why the file itself would present a problem. I have run g_saltbr on similarly sized systems. Sorry, I can't offer an explanation as to why it's stopping prematurely. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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_saltbr speed
Dear Gromacs users, I was running the saltbridge calculations for a dimeric protein simulation using g_saltbr, But its taking very long time, almost four days still its not completed. Could anyone has suggestion regarding this issue? I am using the same system - Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz where i ran MD. Please give some suggestion as to how to increase the speed of calculation. Command i issued was: g_saltbr -f ../traj.xtc -s md.tpr -t 0.4 -sep Thank you Kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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_saltbr speed
Dear Sir, That is true as the number of the frames increased the memory had almost reached 95% but still it has been in 95% since long and CPU usage drops down to 1.5 -2 % but in many cases i have seen that still it will run (off course slowly) and finish. But this was too long. So any suggestions? Thank you Kavya On Thu, Jul 12, 2012 at 3:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 4:51 AM, Kavyashree M wrote: Dear Gromacs users, I was running the saltbridge calculations for a dimeric protein simulation using g_saltbr, But its taking very long time, almost four days still its not completed. Could anyone has suggestion regarding this issue? I am using the same system - Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz where i ran MD. Please give some suggestion as to how to increase the speed of calculation. Command i issued was: g_saltbr -f ../traj.xtc -s md.tpr -t 0.4 -sep g_saltbr calculates properties of all possible ionic pairs in the system, so if there are many, the calculation might take a long time. Four days sounds ridiculous, and perhaps the program has frozen by exhausting the available memory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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_saltbr speed
Thanks :). will check whether it makes it faster. On Thu, Jul 12, 2012 at 4:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 6:38 AM, Kavyashree M wrote: Dear Sir, That is true as the number of the frames increased the memory had almost reached 95% but still it has been in 95% since long and CPU usage drops down to 1.5 -2 % but in many cases i have seen that still it will run (off course slowly) and finish. But this was too long. So any suggestions? http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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_saltbr speed
Dear Sir, I had a problem again during g_saltbr calculation it needs .xtc and .tpr file, I can reduce the .xtc file to have only protein but .tpr file will have water also in it. inorder to generate new tpr file without water using grompp, i need topology file without water .. so do you suggest me to go this way.. it appears quite complicated! Thank you Kavya On Thu, Jul 12, 2012 at 4:52 PM, Kavyashree M hmkv...@gmail.com wrote: Thanks :). will check whether it makes it faster. On Thu, Jul 12, 2012 at 4:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 6:38 AM, Kavyashree M wrote: Dear Sir, That is true as the number of the frames increased the memory had almost reached 95% but still it has been in 95% since long and CPU usage drops down to 1.5 -2 % but in many cases i have seen that still it will run (off course slowly) and finish. But this was too long. So any suggestions? http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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_saltbr speed
I read that. but while executing tpbconv i did not see where i can specify that i do not want solvent? Thanks Kavya On Thu, Jul 12, 2012 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 8:15 AM, Kavyashree M wrote: Dear Sir, I had a problem again during g_saltbr calculation it needs .xtc and .tpr file, I can reduce the .xtc file to have only protein but .tpr file will have water also in it. inorder to generate new tpr file without water using grompp, i need topology file without water .. so do you suggest me to go this way.. it appears quite complicated! In fact, it's quite easy with tpbconv. From tpbconv -h: 3. by creating a .tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your .tpx file, or when you want to make e.g. a pure Calpha .tpx file. Note that you may need to use -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not fully functional. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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_saltbr speed
Ok may be i need to specify an index file. I will try that. And regarding the WARNING: this .tpx file is not fully functional. I hope it will work fine enough to finish g_saltbr calculation? Thanks Kavya On Thu, Jul 12, 2012 at 5:59 PM, Kavyashree M hmkv...@gmail.com wrote: I read that. but while executing tpbconv i did not see where i can specify that i do not want solvent? Thanks Kavya On Thu, Jul 12, 2012 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 8:15 AM, Kavyashree M wrote: Dear Sir, I had a problem again during g_saltbr calculation it needs .xtc and .tpr file, I can reduce the .xtc file to have only protein but .tpr file will have water also in it. inorder to generate new tpr file without water using grompp, i need topology file without water .. so do you suggest me to go this way.. it appears quite complicated! In fact, it's quite easy with tpbconv. From tpbconv -h: 3. by creating a .tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your .tpx file, or when you want to make e.g. a pure Calpha .tpx file. Note that you may need to use -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not fully functional. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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_saltbr speed
Dear Sir, Thank you It worked :). a very usefull suggestion. But it did not promt to choose any option. I used index file. Thank you Kavya On Thu, Jul 12, 2012 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 7/12/12 8:31 AM, Kavyashree M wrote: Ok may be i need to specify an index file. I will try that. And regarding the WARNING: this .tpx file is not fully functional. I hope it will work fine enough to finish g_saltbr calculation? In principle, you should be prompted to choose a default group, but you can also use a custom index group as needed. The warning message is intended to note that the .tpr file you produce will not likely work for running an actual simulation. It should be fine for analysis. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] homodimer simulation
Dear user, I simulated a homodimer of 238aa each with oplsaa forcefield using gromacs-4.5.3. But while calculating the rmsf plot I got a plot in which starting and ending residue were connected by a straight line along with the actual rmsf plot. Also the two rmsf plots that it gave were slightly different from each other in few regions. I was expecting similar rmsf for both the monomers. I checked the pdb file generated after md run, it did not have chain ID but two chains were present. Kindly let me know what is wrong with rmsf? Or what is wrong with simulation. Thanking you With Regards avya -- 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] Number of nodes
Dear Users, I was trying to run a simulation (gromacs4.5.3) on a Bluegene/L machine. But I was unable to run. System admin say that I need to change the input file. I am not sure what needs to be changed in the input file which specifies no. of nodes usage. I am not familiar with the bluegene machines. Kindly suggest the possible solutions. Thanking you With Regards Kavya -- 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 nodes
Hello, System Admin said that the Job fails on 32 and 128 because memory is insufficient for each task, so upon increasing the nodes, data gets distributed across more number of nodes and each node gets less memory occupancy and he also mentioned that he was able to run on 512 nodes but it was giving error for not having sufficient data for 512 nodes. I have run the same job on 8 nodes in i7 machine. Thank you With Regards Kavya On Mon, Oct 31, 2011 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Dear Users, I was trying to run a simulation (gromacs4.5.3) on a Bluegene/L machine. But I was unable to run. System admin say that I need to change the input file. I am not sure what needs to be changed in the input file which specifies no. of nodes usage. Sounds like your system admin should be offering you some more help, since they know the specifics of the hardware, queuing software, etc. I am not familiar with the bluegene machines. Kindly suggest the possible solutions. Without seeing your input file(s), there's nothing anyone can do. Be mindful that this list pertains to Gromacs-specific problems, which do not seem to be present here. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] High temperature Simulation
Hello, Thank you. I got the point but I have a doubt, equilibrate under NPT until the pressure and temperature are stable, then switch to NVT to eliminate the boiling issue, how exactly it will eliminate the boiling issue if we dont use higher pressure while equlibrating? (as you said that it is difficult to simulate at high pressure due to stability reasons.) Thank you With Regards Kavya -- 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] High temperature Simulation
Ok Thanks. On Tue, Oct 18, 2011 at 4:41 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Hello, Thank you. I got the point but I have a doubt, equilibrate under NPT until the pressure and temperature are stable, then switch to NVT to eliminate the boiling issue, how exactly it will eliminate the boiling issue if we dont use higher pressure while equlibrating? (as you said that it is difficult to simulate at high pressure due to stability reasons.) You should equilibrate under whatever the necessary conditions are, be it high pressure or not. Once the desired parameters have been achieved, then switch to NVT. Since the box is invariant in NVT, you don't have to worry about anything expanding. Please continue to search in the literature for finer methodology points. I'm certain these issues have been addressed in greater detail elsewhere. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] High temperature Simulation
Dear users, For simulating a protein at high temperature (more than 300K, less than 400K) using OPLSAA forcefield, what are the parameters other than Temperature that need to be taken care of? Does the energy minimization step also needs to be done at high temperature? (here my aim is not to simulate an unfolding event) I have a reference - Biophysical Journal Volume 94 June 2008 –4453 Any other references or suggestions will be helpful. Thanking you With Regards M. Kavyashree -- 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] High temperature Simulation
Thank you, What about the pressure that need to be used at that temperature (for a system of a protein in tip4p water) Thank you With Regards Kavya On Mon, Oct 17, 2011 at 3:29 PM, bipin singh bipinel...@gmail.com wrote: As far as I know we do energy minimization at room temperature only. Only during equilibration (NVT and NPT) we use high temperature for maintaining proper density before starting the final production run. On Mon, Oct 17, 2011 at 15:15, Kavyashree M hmkv...@gmail.com wrote: Dear users, For simulating a protein at high temperature (more than 300K, less than 400K) using OPLSAA forcefield, what are the parameters other than Temperature that need to be taken care of? Does the energy minimization step also needs to be done at high temperature? (here my aim is not to simulate an unfolding event) I have a reference - Biophysical Journal Volume 94 June 2008 –4453 Any other references or suggestions will be helpful. Thanking you With Regards M. Kavyashree -- 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 -- --- Regards, Bipin Singh -- 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] High temperature Simulation
Hello, The set pressure should reflect whatever system you are trying to model. This statement is not very clear to me.. But when the mdout.mdp file after grompp during energy minimization is examined it says - gen-vel = no gen-temp = 300 gen-seed = 173529 Even though I have not assigned any velocities in em.mdp file. Thats the reason why got this doubt about temperature during energy minimization. Thank you With Regards Kavya -Justin Thank you With Regards Kavya On Mon, Oct 17, 2011 at 3:29 PM, bipin singh bipinel...@gmail.commailto: bipinel...@gmail.com wrote: As far as I know we do energy minimization at room temperature only. Only during equilibration (NVT and NPT) we use high temperature for maintaining proper density before starting the final production run. On Mon, Oct 17, 2011 at 15:15, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, For simulating a protein at high temperature (more than 300K, less than 400K) using OPLSAA forcefield, what are the parameters other than Temperature that need to be taken care of? Does the energy minimization step also needs to be done at high temperature? (here my aim is not to simulate an unfolding event) I have a reference - Biophysical Journal Volume 94 June 2008 –4453 Any other references or suggestions will be helpful. Thanking you With Regards M. Kavyashree -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] High temperature Simulation
Hello, Yes, I have come across that but If the temperature is below the boiling point its fine. But if it crosses the boiling temperature in order keep the water as liquid isnt it necessary to increase the pressure. I understand that the water models do not exactly predict the transition temperature. So in what way does this behaviour of water effect the simulation of a protein? Thank you With Regards kavya On Mon, Oct 17, 2011 at 5:13 PM, bipin singh bipinel...@gmail.com wrote: Well,as I found in literatures people have used same( 1 atm) pressure at high temperature simulations(NPT simulations). with different water models.As most of the force field parameters are determined generally at 300K and 1 atm. What would be the the possible drawbacks of using the same pressure(or even high pressure) at different temperatures(300K-400K ranges) for a given force field. On Mon, Oct 17, 2011 at 17:04, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Thank you, What about the pressure that need to be used at that temperature (for a system of a protein in tip4p water) The set pressure should reflect whatever system you are trying to model. -Justin Thank you With Regards Kavya On Mon, Oct 17, 2011 at 3:29 PM, bipin singh bipinel...@gmail.com mailto:bipinel...@gmail.com wrote: As far as I know we do energy minimization at room temperature only. Only during equilibration (NVT and NPT) we use high temperature for maintaining proper density before starting the final production run. On Mon, Oct 17, 2011 at 15:15, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, For simulating a protein at high temperature (more than 300K, less than 400K) using OPLSAA forcefield, what are the parameters other than Temperature that need to be taken care of? Does the energy minimization step also needs to be done at high temperature? (here my aim is not to simulate an unfolding event) I have a reference - Biophysical Journal Volume 94 June 2008 –4453 Any other references or suggestions will be helpful. Thanking you With Regards M. Kavyashree -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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/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 -- --- Regards, Bipin Singh -- 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