[gmx-users] How does x2top recognize between alkane C and alkene C
Thank you for the response. In case of an all atom representation, the connections are different. What about a united atom representation? The g_x2top supports Gromacs 53a5 forcefield right? Can we get a topology with x2top only for an all atom representation? Or is there anyway to get it for gromos or opls ua ? Thanks and Regards Sridhar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LJ-14 energy
On 7/15/15 8:39 PM, Ming Tang wrote: Dear Chaban and Justin, Sorry for the mis-action. Please ignore my last email. Thank you both for your free help. I am pulling a collagen triple helix in a periodic water box using umbrella direction-periodic. I want to calculate the Lennard-Jones 12-6 of the protein. According to Gromacs manual, it contains repulsive short-range term and attractive long-range term. Is the Lennard-Jones 12-6 energy simply the addition of LJ-SR and LJ-LR? I am interested in the energy trends more than LJ-LR only exists with a twin-range cutoff approach. The total LJ between any groups also includes LJ-14 for intramolecular terms. Intermolecular LJ would be the sum of LJ-SR and LJ-LR, if the latter exists. the energy absolute values. So, if I can calculate the LJ 12-6 of the whole system, it is fine, because I can assume the energy of the water is not subject to change due to pulling. Why can you assume that? You're pulling a structure, which is a non-equilibrium process. There will be different interactions as a function of time. Water-water interactions at long distance from the protein indeed are unlikely to be affected, but those close to the protein may be different (though electrostatics/hydrogen bonding are probably much more interesting). Water-protein interactions certainly can't be assumed to be unchanging during pulling. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] LJ-14 energy
Dear Gromacs experts, I am confused about the meaning of LJ-14 option in g_energy. I checked the achieve, and found that Justin said it stands for intramolecular interactions between atoms separated by 3 bonds. My simulation is protein solvated in water. How can I calculate the Lennard-Jones potential energy of the whole system? I found that if I set 2 energy groups and rerun, there will be options like LJ-14: protein-ions. So, how does Gromacs calculate those energy? Another problem I came across is the LJ-14 I got is weird. The Coulomb-14 energy decrease from 5e4 to 3.8e4, but LJ-14 energy decrease from -400 to -700 and then increase to- 400, followed by a linear decline to -1700. The LJ-14 should increase, am I right? Here is part of my .mdp cutoff-scheme= verlet ns_type = grid coulombtype = reaction-field coulomb-modifier = potential-shift rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_rf = 61 vdwtype = cut-off vdw-modifier = force-switch rvdw-switch = 0.8 rvdw = 1.4 To find out the reason, I checked the manual. It says for vdwtype = switch or vdw-modifier = Potential - switch, rlist should be 0.1 - 0.3 larger than rvdw. As I did not set verlet-buffer-tolerance = -1, gromcas set rlist =1 for the simulation automatically, which is not 0.1 - 0.3 larger than rvdw. Is this the reason of the weird LJ-14? Another question is, is vdw-modifier = force switch more accurate than vdw-modifier = potential - shift? Any help will be appreciated. Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Expected Performance of a GPU workstation
Hi Jason, you might want to take a look at this study: http://arxiv.org/abs/1507.00898 Best, Carsten On 15 Jul 2015, at 06:44, Jason Loo Siau Ee jasonsiauee@taylors.edu.my wrote: Dear Gromacs users, I'm thinking about purchasing a GPU workstation for some simulation work, and was wondering about the optimal CPU-GPU combination for running MD as I'm pretty clueless about the hardware side of things. Typical systems simulated would be membrane protein systems of around 100k atoms, with PME electrostatics. Assuming I have a budget of approximately 7000USD for the machine, what sort of CPU-GPU combination would you recommend? If I went with something like 2x Intel(r) Xeon(r) Processor E5-2695 v2, 12 cores + 2x GTX980s, how many ns/day can I reasonably expect? Has anyone had experience with similar systems? Thanks in advance for the info. Cheers, Jason Confidentiality Disclaimer: This e-mail and any attachments are confidential and intended solely for the intended addressee and may also be privileged or exempt from disclosure under applicable law. If you are not the intended addressee, or have received this e-mail in error, please notify the sender immediately, delete it from your system and do not copy, disclose, distribute or otherwise act in reliance upon any part of this e-mail or its attachments. Taylor's Education Group does not accept responsibility for any loss arising from unauthorized access to, or interference with, any internet communications by any third party in reliance to this email, or from the transmission of any viruses. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of Taylor's Education Group. Replies to this e-mail may be monitored by Taylor's Education Group for operational or business reasons. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48
I was experiencing something similar with 1-1-48, and after switching back to 1-1-6 my system ran fine There's a discussion on Redmine about it (see the last couple of posts): http://redmine.gromacs.org/issues/1770 This doesn't solve your issue, but it indicates that you may be experiencing a bug when you use 1-1-48. -- James “Wes” Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Julian Zachmann frankjulian.zachm...@uab.cat Sent: Wednesday, July 15, 2015 11:51 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48 It just crashes... Without any error message. I am now re-running the simulations with fewer lambda points and for 5ns. Let's see what comes up. 2015-07-15 18:12 GMT+02:00 Barnett, James W jbarn...@tulane.edu: Do you get any output with the crash? Or is it just a segmentation fault? -- James “Wes” Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Julian Zachmann frankjulian.zachm...@uab.cat Sent: Wednesday, July 15, 2015 9:20 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48 Dear Gromacs Users, I am running free energy calculations (FEP) to estimate relative binding affinities. So far, my results don't match the experimental results (not even close), so I must be doing something wrong. My protocol is the following: - Energy minimisation - Leap frog minimisation - 0.1ns NVT - 2nsSimulated Annealing up to 350K - 0.1ns NPT - 1ns MD production run During the whole equilibration time I am using umbrella pulling to maintain an interaction between one residue and the ligand (especially important during SA) but I remove it for MD because I am afraid it would influence my results (even though I don't know it for sure). The simulation time for 1ns is quite short of course but I have 'nstdhdl' put to 10 to get a lot of output. The other settings are pasted below. So far I was using 1-1-6 for the soft core potential but because the results were not good, I was thinking to try 1-1-48. However in this case the simulations always crash. Has anybody run successfully 1-1-48 soft core potentials in Gromacs and how did you chose your settings? Like me pasted below? Any other suggestions about what I am doing wrong? Could I maintain the pull distance constraint during the MD simulation? Best regards, Julian free_energy = yes init_lambda_state= $i ; 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 fep_lambdas = 0. 0.0300 0.0600 0.0900 0.1200 0.1500 0.1800 0.2100 0.2400 0.2700 0.3000 0.3300 0.3600 0.3900 0.4200 0.4500 0.4800 0.5100 0.5400 0.5700 0.6000 0.6300 0.6600 0.6900 0.7200 0.7500 0.7800 0.8100 0.8400 0.8700 0.9000 0.9300 0.9600 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. vdw_lambdas = 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.0500 0.1000 0.1500 0.2000 0.2500 0.3000 0.3500 0.4000 0.4500 0.5000 0.5500 0.6000 0.6500 0.7000 0.7500 0.8000 0.8200 0.8500
[gmx-users] clarification regarding input format for g_kinetics
I was looking to use g_kinetics, and was slightly confused by the input options, and was hoping someone could help clarify. An example case of using g_kinetics is: g_kinetics -f temp.xvg -d data.xvg -o ft_all.xvg -o2 it_all.xvg -o3 ft_repl.xvg -m melt.xvg -ee err_est.xvg From what I can ascertain, temp.xvg is generated from using the demux.pl script (the output file remd_temps.xvg?); and I know data.xvg should be a flat file that has an indicator of folding/unfolding in it; however, what I am confused about is should data.xvg be a multi-column file with the first column being time followed by one column per demuxed replica trajectory of the current state of the indicator, i.e 1 if folded and 0 unfolded. Something that looks like this 0 1 1 1 0 0 0 0 1 1 0 0 1 0 0 1 ... and so on. Thanks in advanced for the help. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Errors There were 2 inconsistent shifts. Check your topology after I moved my peptide with VMD
Hello, I used my charmm-gui.org built system on Gromacs for some time. Then I tried to adjust it little bit and moved my peptide with VMD to other place. I am not sure it is fine because I can get clashes and so on, but I tried it. I want to reuse same topology. Now try to minimize it again and get error:There were 2 inconsistent shifts. Check your topologyMaybe there is easy way to fix this? Or I have to rebuild everything from 0? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Expected Performance of a GPU workstation
Dear Carsten, That pretty much covers all my questions and then some. Thanks for that! Cheers, Jason -- Hi Jason, you might want to take a look at this study: http://arxiv.org/abs/1507.00898 Best, Carsten On 15 Jul 2015, at 06:44, Jason Loo Siau Ee jasonsiauee@taylors.edu.my wrote: Dear Gromacs users, I'm thinking about purchasing a GPU workstation for some simulation work, and was wondering about the optimal CPU-GPU combination for running MD as I'm pretty clueless about the hardware side of things. Typical systems simulated would be membrane protein systems of around 100k atoms, with PME electrostatics. Assuming I have a budget of approximately 7000USD for the machine, what sort of CPU-GPU combination would you recommend? If I went with something like 2x Intel(r) Xeon(r) Processor E5-2695 v2, 12 cores + 2x GTX980s, how many ns/day can I reasonably expect? Has anyone had experience with similar systems? Thanks in advance for the info. Cheers, Jason Confidentiality Disclaimer: This e-mail and any attachments are confidential and intended solely for the intended addressee and may also be privileged or exempt from disclosure under applicable law. If you are not the intended addressee, or have received this e-mail in error, please notify the sender immediately, delete it from your system and do not copy, disclose, distribute or otherwise act in reliance upon any part of this e-mail or its attachments. Taylor's Education Group does not accept responsibility for any loss arising from unauthorized access to, or interference with, any internet communications by any third party in reliance to this email, or from the transmission of any viruses. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of Taylor's Education Group. Replies to this e-mail may be monitored by Taylor's Education Group for operational or business reasons. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Deformation of DNA duplex
I am not sure if GROMACS can do that type of analysis. But I think 3DNA should be able to compute the different base pair step parameters. Debayan On Wed, Jul 15, 2015 at 4:12 PM, soumadwip ghosh soumadwipgh...@gmail.com wrote: Hi all, I have a couple of quick questions. I am simulating DNA duplex with some fullerene derivatives. The fullerenes are expected to accommodate themselves in the major groove of the DNA and I am getting similar results. However, the parallel DNA chains are getting deformed which is also expected. My question is apart from H-bonds is there any way by which one can show that the DNA is getting significantly deformed as compared to its native structure? In the given link below, people have used roll, twist, curl and slides to probe the DNA deformation. Is there any way I can calculate those parameters from GROMACS? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439907/pdf/gks517.pdf How can I show the time evolution of fraction of native contacts for my DNA chain? Sorry if I am asking for much. Thanks for your time in advance. Regards, Soumadwip Ghosh Research Fellow, IITB India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'
Justin, Thanks for the response, I have started to use pure OpenMP parallelization which has solved the issue with DD. Somehow I missed this detail about domain decomposition when reading about parallelization with tMPI vs OpenMP. John On Thu, Jun 25, 2015 at 6:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/25/15 2:46 PM, John Degenstein wrote: Justin, Ok, so I decided to take a different path to solve this issue. Essentially, using the Berendsen Pcoupl the system should condense under high pressure. For some reason it does not seem to work very quickly at least. To get around this issue I running several steps of equilibration EM followed by NVT at 600K followed by NPT at 100bar with the Berendsen Pcoupl. I think using a higher temperature helps to increase the velocity of my larger (than water) molecules and thus improve the rate of condensation. After this I do another stage of NVT at 300K to get a new velocity distribution followed by NPT with Parrinello-Rahman at 1 bar. One issue I have faced is that too many steps with Pcoupl set to Parrinello-Rahman leads to the system collapsing rapidly which then causes issues with the number of DD cells relative to the current vs. old size of the box. To solve this issue I restart with a 2nd stage of Parrinello-Rahman again starting from the output structure of the 1st stage of Par-Rah. So far this seems to work well and results in a high and seemingly accurate density with a box that tightly surrounds the cluster. I suppose in retrospect that I could simply use a single processor which I think would reduce the number of DD cells and thus prevent this error. Or just use OpenMP parallelization. Any time you drastically change the size of the system, this will be the case. Does anyone have any thoughts/comments/concerns about my procedure? Seems OK, just equilibrate thoroughly under the new conditions. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48
It just crashes... Without any error message. I am now re-running the simulations with fewer lambda points and for 5ns. Let's see what comes up. 2015-07-15 18:12 GMT+02:00 Barnett, James W jbarn...@tulane.edu: Do you get any output with the crash? Or is it just a segmentation fault? -- James “Wes” Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Julian Zachmann frankjulian.zachm...@uab.cat Sent: Wednesday, July 15, 2015 9:20 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48 Dear Gromacs Users, I am running free energy calculations (FEP) to estimate relative binding affinities. So far, my results don't match the experimental results (not even close), so I must be doing something wrong. My protocol is the following: - Energy minimisation - Leap frog minimisation - 0.1ns NVT - 2nsSimulated Annealing up to 350K - 0.1ns NPT - 1ns MD production run During the whole equilibration time I am using umbrella pulling to maintain an interaction between one residue and the ligand (especially important during SA) but I remove it for MD because I am afraid it would influence my results (even though I don't know it for sure). The simulation time for 1ns is quite short of course but I have 'nstdhdl' put to 10 to get a lot of output. The other settings are pasted below. So far I was using 1-1-6 for the soft core potential but because the results were not good, I was thinking to try 1-1-48. However in this case the simulations always crash. Has anybody run successfully 1-1-48 soft core potentials in Gromacs and how did you chose your settings? Like me pasted below? Any other suggestions about what I am doing wrong? Could I maintain the pull distance constraint during the MD simulation? Best regards, Julian free_energy = yes init_lambda_state= $i ; 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 fep_lambdas = 0. 0.0300 0.0600 0.0900 0.1200 0.1500 0.1800 0.2100 0.2400 0.2700 0.3000 0.3300 0.3600 0.3900 0.4200 0.4500 0.4800 0.5100 0.5400 0.5700 0.6000 0.6300 0.6600 0.6900 0.7200 0.7500 0.7800 0.8100 0.8400 0.8700 0.9000 0.9300 0.9600 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. vdw_lambdas = 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.0500 0.1000 0.1500 0.2000 0.2500 0.3000 0.3500 0.4000 0.4500 0.5000 0.5500 0.6000 0.6500 0.7000 0.7500 0.8000 0.8200 0.8500 0.8700 0.8800 0.8900 0.9000 0.9100 0.9200 0.9300 0.9350 0.9400 0.9450 0.9500 0.9530 0.9570 0.9600 0.9630 0.9670 0.9700 0.9730 0.9770 0.9800 0.9820 0.9840 0.9860 0.9880 0.9900 0.9910 0.9920 0.9930 0.9940 0.9950 0.9955 0.9960 0.9965 0.9970 0.9975 0.9980 0.9983 0.9987 0.9990 0.9992 0.9993 0.9994 0.9995 0.9996 0.9997 0.9998 0. 1. ; 1-1-6 sc-coul= no sc-alpha = 0.5 sc-power = 1 sc-sigma = 0.3 sc-r-power = 6 ; 1-1-48 ;sc-coul = no ; ;sc-alpha = 0.0025 ; either 0.5 (sc-r-power = 6) or 0.0025 (sc-r-power = 48) ;sc-power= 1; 1 or 2 ;sc-sigma= 0.3 ; default 0.3 ;sc-r-power = 48 ; possible 6, 48 calc-lambda-neighbors= -1 nstdhdl = 10 dhdl-derivatives
Re: [gmx-users] position restraining of ions
Hi, this problem usually arises when there are more than one species of a perticular kind is present in your conf.gro file. In your case you have 85 potassium and 122 chloride ions in the input .gro file you used while generating individual ion posre.itp files. However, in the ions.itp file in your FF directory contains one description for K+ and CL- each. If you observe carefully,grompp complains about atomindex starting from 2 that's because genrestr made posre.itp for all the potassium ions in the system ( same with chloride) while in ions.itp there is only one description of both K+ and and CL- . I think the following will help 1. make an index file containing one K+ and one CL- 2. Issue genrestr with -n flag 3. when prompted use these two indices with one residue each separately 4. Make separate posre.itp for both the species 5. They should not contain more than a line 6. Include these two .itp files with proper IFDEF statements in the system.top . I dont think you will see the error after this. Cheers Soumadwip -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx distance - COM distance issue
Hi Justin, First of all, thanks a lot for your reply. I saw during the simulation that; indeed, the protein positioned in a corner of the simulation box, so i ‘refined’ the trajectory by centering the protein. And now, the gmx distance method gave me more ‘logical’ distances with respect the adsorption process of the protein into the bilayer. Thanks a lot. Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl On July 15, 2015 at 10:28:42 AM, Justin Lemkul (jalem...@vt.edumailto:jalem...@vt.edu) wrote: On 7/14/15 10:33 PM, Carlos Navarro Retamal wrote: Dear gmx users, In an attempt to analyse the interaction between a Protein and a Bilayer (in a CG MD simulations) i’m using gmx distance as following: gmx distance -f DFMG-200ns.xtc -s DFMG-200ns.tpr -n index.ndx -select 'com of group Protein plus com of group Membranes' -oall distance.xvg. By analysing the CONTACTS between both macromolecules i now that the protein interact peripherally with the membrane (moving from the aqueous solution to the membrane), by interacting with the head group of the bilayer. My problem is that, contrary to what i might imagine, base on the ‘distance’ analysis i’m seeing that the distance between the molecules increase during time: beginning: 0.000 4.062 100.000 3.952 200.000 3.768 300.000 3.576 400.000 3.422 500.000 3.526 600.000 3.561 700.000 3.619 800.000 3.643 900.000 3.682 end: 199100.000 5.347 199200.000 5.244 199300.000 5.273 199400.000 5.410 199500.000 5.369 199600.000 5.275 199700.000 5.415 199800.000 5.525 199900.000 5.557 20.000 5.441 I tried using the -pbc flag (when i used gmx distance) without luck (i got the same values as before). What could be the reason? Because only the vertical dimension (presumably z here in the case of a membrane) is relevant. The protein can still be peripherally associated at a corner of the box, which would have a large COM distance but small z component, indicating binding. Use -oxyz instead of -oall. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] [gm.-users] LJ-14 energy
Dear Chaban and Justin, Thank you both for your free help. I am pulling a collagen triple helix in a periodic water box using umbrella direction-periodic. I want to calculate the Lennard-Jones 12-6 of the protein. According to Gromacs manual, it contains repulsive short-range term and attractive long-range term. Is the Lennard-Jones 12-6 energy -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Wednesday, 15 July 2015 11:36 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] LJ-14 energy On 7/15/15 5:27 AM, Ming Tang wrote: Dear Gromacs experts, I am confused about the meaning of LJ-14 option in g_energy. I checked the achieve, and found that Justin said it stands for intramolecular interactions between atoms separated by 3 bonds. My simulation is protein solvated in water. How can I calculate the Lennard-Jones potential energy of the whole system? I found that if I set 2 energy groups and rerun, there will be options like LJ-14: protein-ions. So, how does Gromacs calculate those energy? Intermolecular LJ-14 are by definition zero and actually do not correspond to anything real, anyway. Just a quirk of the decomposition of nonbonded terms in the code. -Justin This does make sense! Your explanation is always clear and precious. I found that LJ-14: protein-ions of my system is really zero. Another problem I came across is the LJ-14 I got is weird. The Coulomb-14 energy decrease from 5e4 to 3.8e4, but LJ-14 energy decrease from -400 to -700 and then increase to- 400, followed by a linear decline to -1700. The LJ-14 should increase, am I right? Depends on what's happening. There's no reason to think that any energy term will inherently show any trend, but the outcome reflects whatever is happening in the dynamics. Here is part of my .mdp cutoff-scheme= verlet ns_type = grid coulombtype = reaction-field coulomb-modifier = potential-shift rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_rf = 61 vdwtype = cut-off vdw-modifier = force-switch rvdw-switch = 0.8 rvdw = 1.4 To find out the reason, I checked the manual. It says for vdwtype = switch or vdw-modifier = Potential - switch, rlist should be 0.1 - 0.3 larger than rvdw. As I did not set verlet-buffer-tolerance = -1, gromcas set rlist =1 for the simulation automatically, which is not 0.1 - 0.3 larger than rvdw. Is this the reason of the weird LJ-14? I think you're mis-reading the manual. If you set verlet-buffer-tolerance = -1, whatever value of rlist you specify (which you haven't shown, so it defaults to 1) is used. You say you did *not* set verlet-buffer-tolerance explicitly, so it defaults to a value of 0.005 and rlist is tuned as needed. The .log file will have information as to what rlist was used. -Justin I did not set value for verlet-buffer-tolerance and rlist. It turns out that I made a silly mistake. I checked the mdout.mdp rather than the mg.log file for rlist value. According to mg.log file, Gromacs set rlist = 1.47, which is just 0.7 larger than rvdw = 1.4. Is this possible to cause any accuracy problems for LJ energy? Another question is, is vdw-modifier = force switch more accurate than vdw-modifier = potential - shift? The method used depends on what the force field needs. -Justin I use GROMOS 54a7 force field. In the paper defining this ff, I only found the method and parameters used to calculate coulomb force, but did not see those for van der waals force. Therefore, I randomly chose vdwtype = cut-off and vdw-modifier = force switch. Can you give me some guidance about which method and parameters used to calculate the vdw interaction are more suitable for GROMOS 54a7 ff? -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
Re: [gmx-users] Position restraining of ions.
On 7/15/15 11:53 AM, anu chandra wrote: Dear Gromcacs users, I have carried out 25 ns simulation of membrane-protein systems. Now, I would like to do position restrain of ions for the next 1-2 ns. I have KCl in my system. I used ' genrestr ' for generating the position restrain for ions using the following command - genrestr -f md50.gro -o ions-rest.itp I have included ions-rest.itp in the .top file with proper ' ifdef ' term as mention in tutorials. Unfortunately, the grommp shows error message - Atom index (2) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to . I have seen from Gromcas mail list that many faced similar issues and this usually comes from the mismatch in atom indices. Unfortunately, I could not find complete solution for it yet. Few queries in this regard are, 1. How can I generate a position restrain file for ions or any set of molecules in the system? my topology file have following hierarchy, ; This is a standalone topology file ; ; Created by: ; GROMACS: gmx pdb2gmx, VERSION 5.0.4 ; Executable: /usr/local/gromacs/bin/gmx ; Library dir: /usr/local/gromacs/share/gromacs/top ; Command line: ; gmx pdb2gmx -f step5_IP3R.pdb -ter ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include charmm36-jun2015.ff/forcefield.itp ; Include chain topologies #include topol_Protein.itp #include topol_Protein2.itp #include topol_Protein3.itp #include topol_Protein4.itp #include POPC.itp ; Include water topology #include charmm36-jun2015.ff/tip3p.itp ; Include topology for ions #include charmm36-jun2015.ff/ions.itp [ system ] ; Name Titile [ molecules ] ; Compound#mols Protein 1 Protein21 Protein31 Protein41 POPC 295 POT 85 CL 122 SOL24892 2. Where all I can use the .itp file for a particular group generate with ' genrestr' command? Restraints are applied on a per-moleculetype basis; hence genrestr is very limited in what it can do (multiple molecules won't work without considerable effort). The only way to restrain the ions within this setup is to modify ions.itp to specify restraints within the relevant [moleculetype] directives. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to treat c=c double bonds in gromos54a7 forcefield
On 7/15/15 9:52 AM, Isser, Ariel Y. wrote: Hi, I noticed in the gromos54a7.ff folder that the .itp file for the lipid popc written to correspond with the gromos54a7 forcefield treats the covalent bond interactions of c=c double bonds the same as the .rtp entry for aromatic c=n bonds. Is this the proper way of handling c=c double bonds or is there a more precise alternative. Many bonded parameters are shared between different moieties. If this is what is in the force field, this is what has been parametrized and found to be adequate according to its authors. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] LJ-14 energy
Dear Chaban and Justin, Sorry for the mis-action. Please ignore my last email. Thank you both for your free help. I am pulling a collagen triple helix in a periodic water box using umbrella direction-periodic. I want to calculate the Lennard-Jones 12-6 of the protein. According to Gromacs manual, it contains repulsive short-range term and attractive long-range term. Is the Lennard-Jones 12-6 energy simply the addition of LJ-SR and LJ-LR? I am interested in the energy trends more than the energy absolute values. So, if I can calculate the LJ 12-6 of the whole system, it is fine, because I can assume the energy of the water is not subject to change due to pulling. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.semailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Wednesday, 15 July 2015 11:36 PM To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: Re: [gmx-users] LJ-14 energy On 7/15/15 5:27 AM, Ming Tang wrote: Dear Gromacs experts, I am confused about the meaning of LJ-14 option in g_energy. I checked the achieve, and found that Justin said it stands for intramolecular interactions between atoms separated by 3 bonds. My simulation is protein solvated in water. How can I calculate the Lennard-Jones potential energy of the whole system? I found that if I set 2 energy groups and rerun, there will be options like LJ-14: protein-ions. So, how does Gromacs calculate those energy? Intermolecular LJ-14 are by definition zero and actually do not correspond to anything real, anyway. Just a quirk of the decomposition of nonbonded terms in the code. -Justin This does make sense! Your explanation is always clear and precious. I found that LJ-14: protein-ions of my system is really zero. Another problem I came across is the LJ-14 I got is weird. The Coulomb-14 energy decrease from 5e4 to 3.8e4, but LJ-14 energy decrease from -400 to -700 and then increase to- 400, followed by a linear decline to -1700. The LJ-14 should increase, am I right? Depends on what's happening. There's no reason to think that any energy term will inherently show any trend, but the outcome reflects whatever is happening in the dynamics. Here is part of my .mdp cutoff-scheme= verlet ns_type = grid coulombtype = reaction-field coulomb-modifier = potential-shift rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_rf = 61 vdwtype = cut-off vdw-modifier = force-switch rvdw-switch = 0.8 rvdw = 1.4 To find out the reason, I checked the manual. It says for vdwtype = switch or vdw-modifier = Potential - switch, rlist should be 0.1 - 0.3 larger than rvdw. As I did not set verlet-buffer-tolerance = -1, gromcas set rlist =1 for the simulation automatically, which is not 0.1 - 0.3 larger than rvdw. Is this the reason of the weird LJ-14? I think you're mis-reading the manual. If you set verlet-buffer-tolerance = -1, whatever value of rlist you specify (which you haven't shown, so it defaults to 1) is used. You say you did *not* set verlet-buffer-tolerance explicitly, so it defaults to a value of 0.005 and rlist is tuned as needed. The .log file will have information as to what rlist was used. -Justin I did not set value for verlet-buffer-tolerance and rlist. It turns out that I made a silly mistake. I checked the mdout.mdp rather than the mg.log file for rlist value. According to mg.log file, Gromacs set rlist = 1.47, which is just 0.7 larger than rvdw = 1.4. Is this possible to cause any accuracy problems for LJ energy? Another question is, is vdw-modifier = force switch more accurate than vdw-modifier = potential - shift? The method used depends on what the force field needs. -Justin I use GROMOS 54a7 force field. In the paper defining this ff, I only found the method and parameters used to calculate coulomb force, but did not see those for van der waals force. Therefore, I randomly chose vdwtype = cut-off and vdw-modifier = force switch. Can you give me some guidance about which method and parameters used to calculate the vdw interaction are more suitable for GROMOS 54a7 ff? -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edumailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] clarification regarding input format for g_kinetics
On 15/07/15 18:24, Smith, Micholas D. wrote: Just tried it. Seems to work. To be clear, the data.xvg file should created from the demuxed trajectories, right? Yes. Thanks for the help. Sorry for a kind of silly question. Not silly at all, not many people use this I'm afraid. Please check your results anyway. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of David van der Spoel sp...@xray.bmc.uu.se Sent: Wednesday, July 15, 2015 12:13 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] clarification regarding input format for g_kinetics On 15/07/15 14:20, Smith, Micholas D. wrote: I was looking to use g_kinetics, and was slightly confused by the input options, and was hoping someone could help clarify. An example case of using g_kinetics is: g_kinetics -f temp.xvg -d data.xvg -o ft_all.xvg -o2 it_all.xvg -o3 ft_repl.xvg -m melt.xvg -ee err_est.xvg From what I can ascertain, temp.xvg is generated from using the demux.pl script (the output file remd_temps.xvg?); and I know data.xvg should be a flat file that has an indicator of folding/unfolding in it; however, what I am confused about is should data.xvg be a multi-column file with the first column being time followed by one column per demuxed replica trajectory of the current state of the indicator, i.e 1 if folded and 0 unfolded. Something that looks like this 0 1 1 1 0 0 0 0 1 1 0 0 1 0 0 1 That looks OK. Have you tried it? ... and so on. Thanks in advanced for the help. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehxxp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at hxxp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read hxxp://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit hxxps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48
Dear Gromacs Users, I am running free energy calculations (FEP) to estimate relative binding affinities. So far, my results don't match the experimental results (not even close), so I must be doing something wrong. My protocol is the following: - Energy minimisation - Leap frog minimisation - 0.1ns NVT - 2nsSimulated Annealing up to 350K - 0.1ns NPT - 1ns MD production run During the whole equilibration time I am using umbrella pulling to maintain an interaction between one residue and the ligand (especially important during SA) but I remove it for MD because I am afraid it would influence my results (even though I don't know it for sure). The simulation time for 1ns is quite short of course but I have 'nstdhdl' put to 10 to get a lot of output. The other settings are pasted below. So far I was using 1-1-6 for the soft core potential but because the results were not good, I was thinking to try 1-1-48. However in this case the simulations always crash. Has anybody run successfully 1-1-48 soft core potentials in Gromacs and how did you chose your settings? Like me pasted below? Any other suggestions about what I am doing wrong? Could I maintain the pull distance constraint during the MD simulation? Best regards, Julian free_energy = yes init_lambda_state= $i ; 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 fep_lambdas = 0. 0.0300 0.0600 0.0900 0.1200 0.1500 0.1800 0.2100 0.2400 0.2700 0.3000 0.3300 0.3600 0.3900 0.4200 0.4500 0.4800 0.5100 0.5400 0.5700 0.6000 0.6300 0.6600 0.6900 0.7200 0.7500 0.7800 0.8100 0.8400 0.8700 0.9000 0.9300 0.9600 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. vdw_lambdas = 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.0500 0.1000 0.1500 0.2000 0.2500 0.3000 0.3500 0.4000 0.4500 0.5000 0.5500 0.6000 0.6500 0.7000 0.7500 0.8000 0.8200 0.8500 0.8700 0.8800 0.8900 0.9000 0.9100 0.9200 0.9300 0.9350 0.9400 0.9450 0.9500 0.9530 0.9570 0.9600 0.9630 0.9670 0.9700 0.9730 0.9770 0.9800 0.9820 0.9840 0.9860 0.9880 0.9900 0.9910 0.9920 0.9930 0.9940 0.9950 0.9955 0.9960 0.9965 0.9970 0.9975 0.9980 0.9983 0.9987 0.9990 0.9992 0.9993 0.9994 0.9995 0.9996 0.9997 0.9998 0. 1. ; 1-1-6 sc-coul= no sc-alpha = 0.5 sc-power = 1 sc-sigma = 0.3 sc-r-power = 6 ; 1-1-48 ;sc-coul = no ; ;sc-alpha = 0.0025 ; either 0.5 (sc-r-power = 6) or 0.0025 (sc-r-power = 48) ;sc-power= 1; 1 or 2 ;sc-sigma= 0.3 ; default 0.3 ;sc-r-power = 48 ; possible 6, 48 calc-lambda-neighbors= -1 nstdhdl = 10 dhdl-derivatives = yes separate-dhdl-file = yes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48
I put in 1-1-48, and although somewhat more efficient (20-30%), it has a tendency to have floating point errors in single precision. I'll probably take it out sometime in the next few versions, as the benefit is not really worth the hassle. If you are off by a lot, it's almost certainly not going to help. Whether something matches experiment is independent of whether the calculation is performed correctly. If it's off by 2-3 kcal/mol, that could just be the nature of the problem. If it's off by 5-10 kcal/mol, especially for a relative calculation, there is probably something else wrong. Possibly it has to do with your top file, but of course hard to say. 100 lambda states is almost certainly more than needed. When I disappear 60 heavy atoms, I use only 40 lambda points! If you are changing 1-5 heavy atoms, no more than 20 lambda would be needed, 10-12 is probably enough. If there is a lot of protein motion, 1 ns is likely not long enough. I am using umbrella pulling to maintain an interaction between one residue and the ligand (especially important during SA) but I remove it for MD because I am afraid it would influence my results (even though I don't know it for sure). It probably would affect something during MD, but what the effect would be depends on many factors. On Wed, Jul 15, 2015 at 10:20 AM, Julian Zachmann frankjulian.zachm...@uab.cat wrote: Dear Gromacs Users, I am running free energy calculations (FEP) to estimate relative binding affinities. So far, my results don't match the experimental results (not even close), so I must be doing something wrong. My protocol is the following: - Energy minimisation - Leap frog minimisation - 0.1ns NVT - 2nsSimulated Annealing up to 350K - 0.1ns NPT - 1ns MD production run During the whole equilibration time I am using umbrella pulling to maintain an interaction between one residue and the ligand (especially important during SA) but I remove it for MD because I am afraid it would influence my results (even though I don't know it for sure). The simulation time for 1ns is quite short of course but I have 'nstdhdl' put to 10 to get a lot of output. The other settings are pasted below. So far I was using 1-1-6 for the soft core potential but because the results were not good, I was thinking to try 1-1-48. However in this case the simulations always crash. Has anybody run successfully 1-1-48 soft core potentials in Gromacs and how did you chose your settings? Like me pasted below? Any other suggestions about what I am doing wrong? Could I maintain the pull distance constraint during the MD simulation? Best regards, Julian free_energy = yes init_lambda_state= $i ; 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 fep_lambdas = 0. 0.0300 0.0600 0.0900 0.1200 0.1500 0.1800 0.2100 0.2400 0.2700 0.3000 0.3300 0.3600 0.3900 0.4200 0.4500 0.4800 0.5100 0.5400 0.5700 0.6000 0.6300 0.6600 0.6900 0.7200 0.7500 0.7800 0.8100 0.8400 0.8700 0.9000 0.9300 0.9600 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. vdw_lambdas = 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.0500 0.1000 0.1500 0.2000 0.2500 0.3000 0.3500 0.4000 0.4500 0.5000 0.5500 0.6000 0.6500 0.7000 0.7500 0.8000 0.8200 0.8500 0.8700 0.8800 0.8900 0.9000 0.9100 0.9200 0.9300 0.9350 0.9400 0.9450 0.9500 0.9530 0.9570 0.9600 0.9630 0.9670 0.9700 0.9730 0.9770 0.9800 0.9820 0.9840 0.9860 0.9880 0.9900 0.9910 0.9920 0.9930 0.9940 0.9950 0.9955 0.9960 0.9965 0.9970 0.9975 0.9980 0.9983 0.9987 0.9990 0.9992 0.9993 0.9994 0.9995 0.9996 0.9997 0.9998 0. 1. ; 1-1-6 sc-coul= no sc-alpha = 0.5
[gmx-users] Position restraining of ions.
Dear Gromcacs users, I have carried out 25 ns simulation of membrane-protein systems. Now, I would like to do position restrain of ions for the next 1-2 ns. I have KCl in my system. I used ' genrestr ' for generating the position restrain for ions using the following command - genrestr -f md50.gro -o ions-rest.itp I have included ions-rest.itp in the .top file with proper ' ifdef ' term as mention in tutorials. Unfortunately, the grommp shows error message - Atom index (2) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to . I have seen from Gromcas mail list that many faced similar issues and this usually comes from the mismatch in atom indices. Unfortunately, I could not find complete solution for it yet. Few queries in this regard are, 1. How can I generate a position restrain file for ions or any set of molecules in the system? my topology file have following hierarchy, ; This is a standalone topology file ; ; Created by: ; GROMACS: gmx pdb2gmx, VERSION 5.0.4 ; Executable: /usr/local/gromacs/bin/gmx ; Library dir: /usr/local/gromacs/share/gromacs/top ; Command line: ; gmx pdb2gmx -f step5_IP3R.pdb -ter ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include charmm36-jun2015.ff/forcefield.itp ; Include chain topologies #include topol_Protein.itp #include topol_Protein2.itp #include topol_Protein3.itp #include topol_Protein4.itp #include POPC.itp ; Include water topology #include charmm36-jun2015.ff/tip3p.itp ; Include topology for ions #include charmm36-jun2015.ff/ions.itp [ system ] ; Name Titile [ molecules ] ; Compound#mols Protein 1 Protein21 Protein31 Protein41 POPC 295 POT 85 CL 122 SOL24892 2. Where all I can use the .itp file for a particular group generate with ' genrestr' command? Many thanks in advance Anu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48
Do you get any output with the crash? Or is it just a segmentation fault? -- James “Wes” Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Julian Zachmann frankjulian.zachm...@uab.cat Sent: Wednesday, July 15, 2015 9:20 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48 Dear Gromacs Users, I am running free energy calculations (FEP) to estimate relative binding affinities. So far, my results don't match the experimental results (not even close), so I must be doing something wrong. My protocol is the following: - Energy minimisation - Leap frog minimisation - 0.1ns NVT - 2nsSimulated Annealing up to 350K - 0.1ns NPT - 1ns MD production run During the whole equilibration time I am using umbrella pulling to maintain an interaction between one residue and the ligand (especially important during SA) but I remove it for MD because I am afraid it would influence my results (even though I don't know it for sure). The simulation time for 1ns is quite short of course but I have 'nstdhdl' put to 10 to get a lot of output. The other settings are pasted below. So far I was using 1-1-6 for the soft core potential but because the results were not good, I was thinking to try 1-1-48. However in this case the simulations always crash. Has anybody run successfully 1-1-48 soft core potentials in Gromacs and how did you chose your settings? Like me pasted below? Any other suggestions about what I am doing wrong? Could I maintain the pull distance constraint during the MD simulation? Best regards, Julian free_energy = yes init_lambda_state= $i ; 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 fep_lambdas = 0. 0.0300 0.0600 0.0900 0.1200 0.1500 0.1800 0.2100 0.2400 0.2700 0.3000 0.3300 0.3600 0.3900 0.4200 0.4500 0.4800 0.5100 0.5400 0.5700 0.6000 0.6300 0.6600 0.6900 0.7200 0.7500 0.7800 0.8100 0.8400 0.8700 0.9000 0.9300 0.9600 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. 1. vdw_lambdas = 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.0500 0.1000 0.1500 0.2000 0.2500 0.3000 0.3500 0.4000 0.4500 0.5000 0.5500 0.6000 0.6500 0.7000 0.7500 0.8000 0.8200 0.8500 0.8700 0.8800 0.8900 0.9000 0.9100 0.9200 0.9300 0.9350 0.9400 0.9450 0.9500 0.9530 0.9570 0.9600 0.9630 0.9670 0.9700 0.9730 0.9770 0.9800 0.9820 0.9840 0.9860 0.9880 0.9900 0.9910 0.9920 0.9930 0.9940 0.9950 0.9955 0.9960 0.9965 0.9970 0.9975 0.9980 0.9983 0.9987 0.9990 0.9992 0.9993 0.9994 0.9995 0.9996 0.9997 0.9998 0. 1. ; 1-1-6 sc-coul= no sc-alpha = 0.5 sc-power = 1 sc-sigma = 0.3 sc-r-power = 6 ; 1-1-48 ;sc-coul = no ; ;sc-alpha = 0.0025 ; either 0.5 (sc-r-power = 6) or 0.0025 (sc-r-power = 48) ;sc-power= 1; 1 or 2 ;sc-sigma= 0.3 ; default 0.3 ;sc-r-power = 48 ; possible 6, 48 calc-lambda-neighbors= -1 nstdhdl = 10 dhdl-derivatives = yes separate-dhdl-file = yes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
Re: [gmx-users] Extending Simnulation - how analyze?
@Chaban I not use grompp and the extension not create .trr files. What I have to do? - Learn politeness. On Jul 14, 2015, at 3:56 AM, V.V.Chaban vvcha...@gmail.com wrote: The no-headache route is: mv confout.gro conf.gro grompp mdrun trjcat -f *.trr -o fixed.trr On Mon, Jul 13, 2015 at 6:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What did the .log file report about your attempt to append? Mark On Mon, Jul 13, 2015 at 11:18 PM Andrea Spinelli spinell...@gmail.com wrote: Hi, I’m new user of Gromacs and I need extend a simulation of 1000ps. On Gromacs 5.0.5 I use this command line as tutorial said. gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt -append It produced the md_0_2.tpr , but when I run rms command to watch the state of RMSD, it show only first 1000 ps, not from 0 to 2000 ps. Why? What is the command I have to use? to view rmds I use this command line: gmx rms -s md_0_2.tpr -f md_0_1.xtc -o rmsd.xvg Thanks a lot. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Extending Simnulation - how analyze?
Yes!! It works very good!! Thank you, Mark!! On Jul 14, 2015, at 11:39 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Was that actually your mdrun command line? I think you need gmx mdrun -s md_0_2 -deffnm md_0_1 -cpi md_0_1 (with or without -append) to actually get appending happening. mdrun does not deduce the names of the output files from the contents of the checkpoint file. Mark On Tue, Jul 14, 2015 at 9:47 AM Andrea Spinelli spinell...@gmail.com wrote: Hi Mark, in the .log file there are this lines at the start of the extending. There are: 20587 Atoms Charge group distribution at step 50: 5190 5166 5109 5122 Initial temperature: 319.123 K Started mdrun on rank 0 Sun Jul 12 20:50:29 2015 Step Time Lambda 50 1000.00.0 On Jul 14, 2015, at 9:32 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, On Tue, Jul 14, 2015 at 8:10 AM Andrea Spinelli spinell...@gmail.com wrote: @Mark The .log report works for 2000 ps. Sure, but you need to look at the bit between 1 ns and 2 ns to find out what happened when you attempted to append. Mark @Chaban I not use grompp and the extension not create .trr files. What I have to do? On Jul 14, 2015, at 3:56 AM, V.V.Chaban vvcha...@gmail.com wrote: The no-headache route is: mv confout.gro conf.gro grompp mdrun trjcat -f *.trr -o fixed.trr On Mon, Jul 13, 2015 at 6:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What did the .log file report about your attempt to append? Mark On Mon, Jul 13, 2015 at 11:18 PM Andrea Spinelli spinell...@gmail.com wrote: Hi, I’m new user of Gromacs and I need extend a simulation of 1000ps. On Gromacs 5.0.5 I use this command line as tutorial said. gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt -append It produced the md_0_2.tpr , but when I run rms command to watch the state of RMSD, it show only first 1000 ps, not from 0 to 2000 ps. Why? What is the command I have to use? to view rmds I use this command line: gmx rms -s md_0_2.tpr -f md_0_1.xtc -o rmsd.xvg Thanks a lot. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
[gmx-users] How to treat c=c double bonds in gromos54a7 forcefield
Hi, I noticed in the gromos54a7.ff folder that the .itp file for the lipid popc written to correspond with the gromos54a7 forcefield treats the covalent bond interactions of c=c double bonds the same as the .rtp entry for aromatic c=n bonds. Is this the proper way of handling c=c double bonds or is there a more precise alternative. Thank you, Ariel Isser -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx distance - COM distance issue
Maybe your protein is not spherical enough to benefit from the center-of-mass-based analysis? Furthermore, was your initial system configuration properly equilibrated? On Tue, Jul 14, 2015 at 11:33 PM, Carlos Navarro Retamal cnava...@utalca.cl wrote: Dear gmx users, In an attempt to analyse the interaction between a Protein and a Bilayer (in a CG MD simulations) i’m using gmx distance as following: gmx distance -f DFMG-200ns.xtc -s DFMG-200ns.tpr -n index.ndx -select 'com of group Protein plus com of group Membranes' -oall distance.xvg. By analysing the CONTACTS between both macromolecules i now that the protein interact peripherally with the membrane (moving from the aqueous solution to the membrane), by interacting with the head group of the bilayer. My problem is that, contrary to what i might imagine, base on the ‘distance’ analysis i’m seeing that the distance between the molecules increase during time: beginning: 0.0004.062 100.0003.952 200.0003.768 300.0003.576 400.0003.422 500.0003.526 600.0003.561 700.0003.619 800.0003.643 900.0003.682 end: 199100.0005.347 199200.0005.244 199300.0005.273 199400.0005.410 199500.0005.369 199600.0005.275 199700.0005.415 199800.0005.525 199900.0005.557 20.0005.441 I tried using the -pbc flag (when i used gmx distance) without luck (i got the same values as before). What could be the reason? Thanks in advance, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx distance - COM distance issue
On 7/14/15 10:33 PM, Carlos Navarro Retamal wrote: Dear gmx users, In an attempt to analyse the interaction between a Protein and a Bilayer (in a CG MD simulations) i’m using gmx distance as following: gmx distance -f DFMG-200ns.xtc -s DFMG-200ns.tpr -n index.ndx -select 'com of group Protein plus com of group Membranes' -oall distance.xvg. By analysing the CONTACTS between both macromolecules i now that the protein interact peripherally with the membrane (moving from the aqueous solution to the membrane), by interacting with the head group of the bilayer. My problem is that, contrary to what i might imagine, base on the ‘distance’ analysis i’m seeing that the distance between the molecules increase during time: beginning: 0.0004.062 100.0003.952 200.0003.768 300.0003.576 400.0003.422 500.0003.526 600.0003.561 700.0003.619 800.0003.643 900.0003.682 end: 199100.0005.347 199200.0005.244 199300.0005.273 199400.0005.410 199500.0005.369 199600.0005.275 199700.0005.415 199800.0005.525 199900.0005.557 20.0005.441 I tried using the -pbc flag (when i used gmx distance) without luck (i got the same values as before). What could be the reason? Because only the vertical dimension (presumably z here in the case of a membrane) is relevant. The protein can still be peripherally associated at a corner of the box, which would have a large COM distance but small z component, indicating binding. Use -oxyz instead of -oall. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Errors There were 2 inconsistent shifts. Check your topology after I moved my peptide with VMD
The easy way is to run an energy minimization. 'steep' 'cg' 'l_bfgs' Perhaps, you will want to freeze some part of your system before to avoid large displacements, if you care. On Wed, Jul 15, 2015 at 7:29 AM, Vytautas Rakeviius vytautas1...@yahoo.com wrote: Hello, I used my charmm-gui.org built system on Gromacs for some time. Then I tried to adjust it little bit and moved my peptide with VMD to other place. I am not sure it is fine because I can get clashes and so on, but I tried it. I want to reuse same topology. Now try to minimize it again and get error:There were 2 inconsistent shifts. Check your topologyMaybe there is easy way to fix this? Or I have to rebuild everything from 0? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to center the molecule with trjconv
On 7/14/15 11:20 PM, Zhenyu Meng wrote: Dear GROMACS users, I want to simulate DNA in a cubic box with water as solvent and visualize it. By using -pbc mol I can see part of the DNA is out of the box so I want to center the DNA in box. But using -center seems destruct the DNA into several parts. I tried to use -pbc mol followed by -center or -center followed by -pbc mol but both cannot center the DNA (the DNA doesn't fall apart but it's still not in the center). I'm curious about the algorithm about -center option. e.g. if I have a pbc cubic box with length of 5, and the COM of the DNA is at (3,3,3), in that way, if I use -center I think all the atoms of the system(including DNA and water) will shift with a vector(-0.5,-0.5,-0.5) to make sure the COM of DNA is now at(2.5,2.5,2.5) (the default boxcenter). Am I correct? Your help will be highly appreciated! For multi-chain molecules it is often helpful/necessary to center on one chain using an index group. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] LJ-14 energy
On 7/15/15 5:27 AM, Ming Tang wrote: Dear Gromacs experts, I am confused about the meaning of LJ-14 option in g_energy. I checked the achieve, and found that Justin said it stands for intramolecular interactions between atoms separated by 3 bonds. My simulation is protein solvated in water. How can I calculate the Lennard-Jones potential energy of the whole system? I found that if I set 2 energy groups and rerun, there will be options like LJ-14: protein-ions. So, how does Gromacs calculate those energy? Intermolecular LJ-14 are by definition zero and actually do not correspond to anything real, anyway. Just a quirk of the decomposition of nonbonded terms in the code. Another problem I came across is the LJ-14 I got is weird. The Coulomb-14 energy decrease from 5e4 to 3.8e4, but LJ-14 energy decrease from -400 to -700 and then increase to- 400, followed by a linear decline to -1700. The LJ-14 should increase, am I right? Depends on what's happening. There's no reason to think that any energy term will inherently show any trend, but the outcome reflects whatever is happening in the dynamics. Here is part of my .mdp cutoff-scheme= verlet ns_type = grid coulombtype = reaction-field coulomb-modifier = potential-shift rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_rf = 61 vdwtype = cut-off vdw-modifier = force-switch rvdw-switch = 0.8 rvdw = 1.4 To find out the reason, I checked the manual. It says for vdwtype = switch or vdw-modifier = Potential - switch, rlist should be 0.1 - 0.3 larger than rvdw. As I did not set verlet-buffer-tolerance = -1, gromcas set rlist =1 for the simulation automatically, which is not 0.1 - 0.3 larger than rvdw. Is this the reason of the weird LJ-14? I think you're mis-reading the manual. If you set verlet-buffer-tolerance = -1, whatever value of rlist you specify (which you haven't shown, so it defaults to 1) is used. You say you did *not* set verlet-buffer-tolerance explicitly, so it defaults to a value of 0.005 and rlist is tuned as needed. The .log file will have information as to what rlist was used. Another question is, is vdw-modifier = force switch more accurate than vdw-modifier = potential - shift? The method used depends on what the force field needs. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48
On Wed, 15 Jul 2015 16:20:25 +0200 Julian Zachmann frankjulian.zachm...@uab.cat wrote: The simulation time for 1ns is quite short of course but I have 'nstdhdl' put to 10 to get a lot of output. To add to what has been said already: increasing the output within a fixed set of time won't give you any more information. Your data is probably highly correlated. You may want to look into a tool like https://github.com/mobleylab/alchemical-analysis if you haven't done already and have a look how much data survives the correlation analysis implemented in there. Also, check for convergence to see if you have still strongly varying gradients/energies. Something as simple as a block analysis can be very effective. Cheers, Hannes. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Drift in Conserved-Energy with Nose-Hoover thermostat
Dear Gromacs Users and Developers, I have a problem regarding energy conservation in my 10ns NVT protein+water+ions (22765 atoms) production (minimization and equilibration for more than 15ns was carried out in NPT before) simulations using a Nose-Hoover thermostat (tau=2.5ps). On first glance everything looks fine - the potential, kinetic and total energy are nearly perfectly constant (with normal fluctuations) - but when I checked the Conserved-Energy quantity that g_energy outputs I had to recognize a significant (nearly perfectly) linear downward drift of this to-be-conserved quantity of around 1.7 kJ/mol/ps (7.48*10^-5 kJ/mol/ps per atom). This appears somehow disturbing to me since I would expect that this Conserved-Energy is the conserved energy of the extended Nose-Hoover Hamiltonian - which should by definition be conserved. If it would be a drift caused by normal round-off error due to single precision I would expect it to grow with Sqrt(N) and not with N (linear) (N=number of steps). So I would like to know if this is a normal behaviour and also what could cause this (buffer size, precision, constraints etc)? Also I would like to know, if I am correct with my guess that the Conserved-Energy quantity is in this case the energy of the extended Nose-Hoover Hamiltonian? The .mdp file is atatched (don't be confused about rlist=1 - since Im using the Verlet-scheme the verlet-buffer-drift option should be by default active and determine the rlist value (Verlet buffer-size) automatically). Best regards, Bernhard ; Run parameters integrator= md; leap-frog integrator nsteps= 1000; 1 ps = 10 ns dt= 0.001; 1 fs ; Output control nstxout= 5000; save coordinates every ps nstvout= 5000; save velocities every ps nstxtcout= 1000; xtc compressed trajectory output every ps nstenergy= 1000; save energies every ps nstlog= 5000; update log file every ps ; Bond parameters continuation= yes; continue from NPT constraint_algorithm = lincs; holonomic constraints constraints= h-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching cutoff-scheme= Verlet; Verlet cutoff-scheme instead of group-scheme (no charge-groups used) ns_type= grid; search neighboring grid cells nstlist= 10; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.12; grid spacing for FFT ; Temperature coupling is on tcoupl= nose-hoover; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 2.52.5; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no ; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; don’t assign velocities from Maxwell distribution -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Deformation of DNA duplex
Hi all, I have a couple of quick questions. I am simulating DNA duplex with some fullerene derivatives. The fullerenes are expected to accommodate themselves in the major groove of the DNA and I am getting similar results. However, the parallel DNA chains are getting deformed which is also expected. My question is apart from H-bonds is there any way by which one can show that the DNA is getting significantly deformed as compared to its native structure? In the given link below, people have used roll, twist, curl and slides to probe the DNA deformation. Is there any way I can calculate those parameters from GROMACS? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439907/pdf/gks517.pdf How can I show the time evolution of fraction of native contacts for my DNA chain? Sorry if I am asking for much. Thanks for your time in advance. Regards, Soumadwip Ghosh Research Fellow, IITB India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] clarification regarding input format for g_kinetics
Just tried it. Seems to work. To be clear, the data.xvg file should created from the demuxed trajectories, right? Thanks for the help. Sorry for a kind of silly question. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of David van der Spoel sp...@xray.bmc.uu.se Sent: Wednesday, July 15, 2015 12:13 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] clarification regarding input format for g_kinetics On 15/07/15 14:20, Smith, Micholas D. wrote: I was looking to use g_kinetics, and was slightly confused by the input options, and was hoping someone could help clarify. An example case of using g_kinetics is: g_kinetics -f temp.xvg -d data.xvg -o ft_all.xvg -o2 it_all.xvg -o3 ft_repl.xvg -m melt.xvg -ee err_est.xvg From what I can ascertain, temp.xvg is generated from using the demux.pl script (the output file remd_temps.xvg?); and I know data.xvg should be a flat file that has an indicator of folding/unfolding in it; however, what I am confused about is should data.xvg be a multi-column file with the first column being time followed by one column per demuxed replica trajectory of the current state of the indicator, i.e 1 if folded and 0 unfolded. Something that looks like this 0 1 1 1 0 0 0 0 1 1 0 0 1 0 0 1 That looks OK. Have you tried it? ... and so on. Thanks in advanced for the help. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehxxp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at hxxp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read hxxp://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit hxxps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
