[gmx-users] virtual sites
Dear Users, I have a system consisting of peptides and a linear carbohydrate. Initially I tried to simulate these peptides using virtual sites and it worked. I can use pdb2gmx for building virtual sites on protein whereas I have an itp file for the carbohydrate. Is it possible to apply virtual site to a carbohydrate along with the peptides? -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- 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] mdrun cpt
On Oct 29, 2013 1:26 AM, Pavan Ghatty pavan.grom...@gmail.com wrote: Now /afterok/ might not work since technically the job is killed due to walltime limits - making it not ok. Hence use -maxh! Mark So I suppose /afterany/ is a better option. But I do appreciate your warning about spamming the queue and yes I will re-read PBS docs. On Mon, Oct 28, 2013 at 5:11 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: Mark, The problem with one .tpr file set for 100ns is that when job number (say) 4 hits the wall limit, it crashes and never gets a chance to submit the next job. So it's not really automated. That's why I suggested -maxh, so you can have an orderly shutdown. (Though if a job can get suspended, that won't always help, because mdrun can't find out about the suspension...) Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. Sure - read your PBS docs and find the environment variable to read so that job 4 knows its ID so it can submit job 5 with an afterok hold on job 4 on it. But don't tell your sysadmins where I live. ;-) Seriously, if you live on this edge, you could spam infinite jobs, which tends to get your account cut off. That's why you want the afterok hold - you only want the next job to start if the exit code from the first script correctly indicates that mdrun exited correctly. Test carefully! Mark But the PBS queuing system is sometime weird and takes a bit of time to recognize a job and give back its jobID. So I could submit job 5 but be unable to change its status to /hold/ because PBS does not return its ID. Another problem is that if resources are available, job 5 could start before I ever get a chance to /hold/ it. On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. You seem to have no need to use grompp, because you don't need to use a workflow that generates multiple .tpr files. Do the equivalent of what the restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr for the whole 100ns run, and then keep doing mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime with or without -append, perhaps with -maxh, keeping whatever manual backups you feel necessary. Then perhaps concatenate your final trajectory files, according to your earlier choices. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? trjconv just operates on the contents of the trajectory file, as modified by things like -b -e and -dt. The .tpr just gives it context, such as atom names. You could give it a .tpr from any point during the run. Mark If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts http://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow
Re: [gmx-users] virtual sites
On 10/29/13 2:21 AM, Neha Gandhi wrote: Dear Users, I have a system consisting of peptides and a linear carbohydrate. Initially I tried to simulate these peptides using virtual sites and it worked. I can use pdb2gmx for building virtual sites on protein whereas I have an itp file for the carbohydrate. Is it possible to apply virtual site to a carbohydrate along with the peptides? Sure, have you tried? Were there problems? -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] Constant-Force Pulling of Ubiquitin
Hi GMX Users, I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin and it's a implicit model. My mdp file for pulling is shown as following. integrator = md dt = 0.001; ps ! nsteps = 50 ; total 500 ps. nstxout = 100 nstvout = 100 nstfout = 100 nstlist = 10 nstlog = 100 nstcalcenergy =100 rlist = 5 rvdw = 5 rcoulomb = 5 coulombtype = cut-off vdwtype = cut-off table-extension = 5 bd_fric = 0 ld_seed = -1 pbc = no ns_type = simple constraints = all-bonds lincs_order = 4 lincs_iter = 1 lincs-warnangle = 30 Tcoupl = v-rescale tau_t = 1.0 tc-grps = Protein ref_t = 300 Pcoupl = no gen_vel = yes gen_temp= 300 gen_seed= 173529 comm_mode = Angular nstcomm =100 ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 5 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = 2.05016 ; Pull code pull= constant_force ;Center of mass pulling using a linear potential and therefore a constant force. pull_geometry = direction pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group1 = Chain_B pull_group0 = Chain_A pull_k1 = -500 ; kJ mol^-1 nm^-2 pull_vec1 = 0.0 0.0 1.0 However, after pulling simulation, it turns out the potential of this system becomes lower rather than higher (from -1 to -2). It's very wired since potential should become larger after pulling. Here is the notification after g_energy: Energy Average Err.Est. RMSD Tot-Drift --- Potential -20734.52301268.47 -1385.71 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties. I wonder whether there is any problem with my mdp file. Thank you so much!! Best, Vivian -- 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] pbc problem
Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region (1)in some frames and is in region (4) in other frames. -- Dear Justin Very thanks for your attention As has already been stated several times, there is no problem at all. The outcome is completely normal, and there are not discrete regions (1) and (4). It is a continuous block of water via PBC. The molecule can freely diffuse throughout it. If outcome is completely normal, Can I use this structure for pmf calculation. I want to calculate potential of mean force, delta G, as a function of the distance between the centers of mass of drug and the centers of mass of bilayer. Best wishes for you. -- 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] Constant-Force Pulling of Ubiquitin
Hi GMX Users, I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin and it's a implicit model. My mdp file for pulling is shown as following. integrator = md dt = 0.001; ps ! nsteps = 50 ; total 500 ps. nstxout = 100 nstvout = 100 nstfout = 100 nstlist = 10 nstlog = 100 nstcalcenergy =100 rlist = 5 rvdw = 5 rcoulomb = 5 coulombtype = cut-off vdwtype = cut-off table-extension = 5 bd_fric = 0 ld_seed = -1 pbc = no ns_type = simple constraints = all-bonds lincs_order = 4 lincs_iter = 1 lincs-warnangle = 30 Tcoupl = v-rescale tau_t = 1.0 tc-grps = Protein ref_t = 300 Pcoupl = no gen_vel = yes gen_temp= 300 gen_seed= 173529 comm_mode = Angular nstcomm =100 ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 5 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = 2.05016 ; Pull code pull= constant_force ;Center of mass pulling using a linear potential and therefore a constant force. pull_geometry = direction pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group1 = Chain_B pull_group0 = Chain_A pull_k1 = -500 ; kJ mol^-1 nm^-2 pull_vec1 = 0.0 0.0 1.0 However, after pulling simulation, it turns out the potential of this system becomes lower rather than higher (from -1 to -2). It's very wired since potential should become larger after pulling. Here is the notification after g_energy: Energy Average Err.Est. RMSD Tot-Drift --- Potential -20734.52301268.47 -1385.71 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties. I wonder whether there is any problem with my mdp file. Thank you so much!! Best, Vivian -- View this message in context: http://gromacs.5086.x6.nabble.com/Constant-Force-Pulling-of-Ubiquitin-tp5012065.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region (1)in some frames and is in region (4) in other frames. With pbc = xyz, you do not have two chunks of water. You have one chunk of water. Where you put the box for visualization is irrelevant to the simulation. You could align one of the box sides with one of the membrane surfaces, and now you will see only one chunk of membrane, and one chunk of water. In that chunk of water the drug goes wherever diffusion takes it, just like it did inside the membrane. Mark -- Dear Justin Very thanks for your attention As has already been stated several times, there is no problem at all. The outcome is completely normal, and there are not discrete regions (1) and (4). It is a continuous block of water via PBC. The molecule can freely diffuse throughout it. If outcome is completely normal, Can I use this structure for pmf calculation. I want to calculate potential of mean force, delta G, as a function of the distance between the centers of mass of drug and the centers of mass of bilayer. Best wishes for you. -- 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] Constant-Force Pulling of Ubiquitin
You want to switch to sd instead of md. On Oct 29, 2013, at 17:43, Vivian ww...@bu.edu wrote: Hi GMX Users, I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin and it's a implicit model. My mdp file for pulling is shown as following. integrator = md dt = 0.001; ps ! nsteps = 50 ; total 500 ps. nstxout = 100 nstvout = 100 nstfout = 100 nstlist = 10 nstlog = 100 nstcalcenergy=100 rlist = 5 rvdw = 5 rcoulomb = 5 coulombtype = cut-off vdwtype = cut-off table-extension = 5 bd_fric = 0 ld_seed = -1 pbc = no ns_type = simple constraints = all-bonds lincs_order = 4 lincs_iter = 1 lincs-warnangle = 30 Tcoupl = v-rescale tau_t = 1.0 tc-grps = Protein ref_t = 300 Pcoupl = no gen_vel = yes gen_temp= 300 gen_seed= 173529 comm_mode = Angular nstcomm =100 ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 5 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = 2.05016 ; Pull code pull= constant_force ;Center of mass pulling using a linear potential and therefore a constant force. pull_geometry = direction pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group1 = Chain_B pull_group0 = Chain_A pull_k1 = -500 ; kJ mol^-1 nm^-2 pull_vec1 = 0.0 0.0 1.0 However, after pulling simulation, it turns out the potential of this system becomes lower rather than higher (from -1 to -2). It's very wired since potential should become larger after pulling. Here is the notification after g_energy: Energy Average Err.Est. RMSD Tot-Drift --- Potential -20734.52301268.47 -1385.71 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties. I wonder whether there is any problem with my mdp file. Thank you so much!! Best, Vivian -- View this message in context: http://gromacs.5086.x6.nabble.com/Constant-Force-Pulling-of-Ubiquitin-tp5012065.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rotacf error
Hello gromacs users, I´m currently tring to calculate S2 order parameters for comparison with nmr data and other simulations. When i try the command for the NH vector: g_rotacf -s ../protein.tpr -d -P 2 -n nh.ndx -f ../protein_fit.xtc -w -noaver It gives me the only half of the residues (NH vectors). It detects the index file with the correct number of atoms, but i only get data for 57 residues. From the log: Group 0 ( NH) has 114 elements Tried a lot o playing with the index file to no sucess. The conversion of the tpr file to a pdb seems to give the correct numbering. Any insights? Thank you very much, Tiago -- 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] virtual sites
On Tue, Oct 29, 2013 at 2:21 AM, Neha Gandhi n.gandh...@gmail.com wrote: Dear Users, I have a system consisting of peptides and a linear carbohydrate. Initially I tried to simulate these peptides using virtual sites and it worked. I can use pdb2gmx for building virtual sites on protein whereas I have an itp file for the carbohydrate. Yes you can modify the top file by hand to use itp files generated in two different ways. Is it possible to apply virtual site to a carbohydrate along with the peptides? If you have an rtp file for you carbohydrate you should be able to run pdb2gmx and then you should also be able to generate vsite. Or you can generate them using your own scripts. Of course you only need them if you have the respective groups (e.g. CH3). Roland -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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
Aw: Re: [gmx-users] Constant-Force Pulling of Ubiquitin
I dont know how well v-rescale works with pulling. It could be after removing some restraints it still had not reached a good equilibrium (ie let it run a while/nanosecound or 5, before pulling it), or maybe generating velocities on start causes more caos than the proteins or system can handle, still it may be the real system minus several initial time frames, ie it either isnt bound from the start as it is in reality or it prefers to be free...But I may be wrong on some of this...so just suggestions. Also, 500 picoseconds is short for measring things, and would probably be dominated by starting velocity for at least 40-80 picoseconds, thus look at how fast it declines...there are some printed standards for protein-protein delG or domain changes of around 3-4 ns to make sure small loop/domain changes are represented in the energy profile. There was (on some comments) talk of making this around 6 ns..but I dont know if there are set real standards for this held fast to (ive read 2 papers with 400 ns to see domain changes with no pull, and a good 5-6 at 4 ns with pulling so?). Stephan Wakins Gesendet:Dienstag, 29. Oktober 2013 um 20:27 Uhr Von:XAvier Periole x.peri...@rug.nl An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Re: [gmx-users] Constant-Force Pulling of Ubiquitin You want to switch to sd instead of md. On Oct 29, 2013, at 17:43, Vivian ww...@bu.edu wrote: Hi GMX Users, I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin and its a implicit model. My mdp file for pulling is shown as following. integrator = md dt = 0.001 ; ps ! nsteps = 50 ; total 500 ps. nstxout = 100 nstvout = 100 nstfout = 100 nstlist = 10 nstlog = 100 nstcalcenergy =100 rlist = 5 rvdw = 5 rcoulomb = 5 coulombtype = cut-off vdwtype = cut-off table-extension = 5 bd_fric = 0 ld_seed = -1 pbc = no ns_type = simple constraints = all-bonds lincs_order = 4 lincs_iter = 1 lincs-warnangle = 30 Tcoupl = v-rescale tau_t = 1.0 tc-grps = Protein ref_t = 300 Pcoupl = no gen_vel = yes gen_temp = 300 gen_seed = 173529 comm_mode = Angular nstcomm =100 ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 5 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = 2.05016 ; Pull code pull = constant_force ;Center of mass pulling using a linear potential and therefore a constant force. pull_geometry = direction pull_start = yes ; define initial COM distance 0 pull_ngroups = 1 pull_group1 = Chain_B pull_group0 = Chain_A pull_k1 = -500 ; kJ mol^-1 nm^-2 pull_vec1 = 0.0 0.0 1.0 However, after pulling simulation, it turns out the potential of this system becomes lower rather than higher (from -1 to -2). Its very wired since potential should become larger after pulling. Here is the notification after g_energy: Energy Average Err.Est. RMSD Tot-Drift --- Potential -20734.5 230 1268.47 -1385.71 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties. I wonder whether there is any problem with my mdp file. Thank you so much!! Best, Vivian -- View this message in context: http://gromacs.5086.x6.nabble.com/Constant-Force-Pulling-of-Ubiquitin-tp5012065.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to
[gmx-users] hydrogen bond analysis
Greeting I'm working on a MD of a ligand-protein complex during 40 ns i want to analyses ligand-protein interaction hydrogen bonds My first question : Should i analyses a minimized frame from clustering of the trajectory or should i analyses hydrogen bond occupancy over trajectory ? My second question : Is it more correct if i do my analysis over the equilibrated phase of MD (based on RMSD, radius of gyration , etc ...) for example the last 10 ns, than doing it over the whole trajectory (40 ns) ?. thanks -- 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] pbc problem
On 10/29/13 12:02 PM, shahab shariati wrote: Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region (1)in some frames and is in region (4) in other frames. -- Dear Justin Very thanks for your attention As has already been stated several times, there is no problem at all. The outcome is completely normal, and there are not discrete regions (1) and (4). It is a continuous block of water via PBC. The molecule can freely diffuse throughout it. If outcome is completely normal, Can I use this structure for pmf calculation. I want to calculate potential of mean force, delta G, as a function of the distance between the centers of mass of drug and the centers of mass of bilayer. Given the inherent symmetry of the system, yes. -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
Re: [gmx-users] g_rotacf error
On 10/29/13 4:02 PM, Tiago Gomes wrote: Hello gromacs users, I´m currently tring to calculate S2 order parameters for comparison with nmr data and other simulations. When i try the command for the NH vector: g_rotacf -s ../protein.tpr -d -P 2 -n nh.ndx -f ../protein_fit.xtc -w -noaver It gives me the only half of the residues (NH vectors). It detects the index file with the correct number of atoms, but i only get data for 57 residues. From the log: Group 0 ( NH) has 114 elements Tried a lot o playing with the index file to no sucess. The conversion of the tpr file to a pdb seems to give the correct numbering. Any insights? Having never used g_rotacf, I can only offer a guess. If you have 114 elements in the index file (an N and an H for each residue, presumably), then that indeed corresponds to 57 residues. Oddly, though, this should not be how g_rotacf works. According to the help description, the index group should be composed of atom triplets. The fact that 114 is evenly divisible by 3 is probably why the command doesn't crash outright. -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
Re: [gmx-users] hydrogen bond analysis
On 10/29/13 5:46 PM, larif sofiene wrote: Greeting I'm working on a MD of a ligand-protein complex during 40 ns i want to analyses ligand-protein interaction hydrogen bonds My first question : Should i analyses a minimized frame from clustering of the trajectory or should i analyses hydrogen bond occupancy over trajectory ? I would think that a time average is much more useful than any single frame. My second question : Is it more correct if i do my analysis over the equilibrated phase of MD (based on RMSD, radius of gyration , etc ...) for example the last 10 ns, than doing it over the whole trajectory (40 ns) ?. Allowing for equilibration time is generally a good idea. -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] Simulate partially hydrolized polyacrylamide in solutions
Hi,everyone, I'm a newcomer, i want to simulate partially hydrolized polyacrylamide in solutions,please give me some suggestions,how to build the polymer pdb structure and how to opitimize the structure, thank U! Qu Guangmiao qugm...@126.com-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Gibbs Energy Calculation and charges
Just want this to make another pass, just in case those in the know missed it. Using couple-intrmol = yes the resulting dH/dl plot actually looks like that at lamba = 1 it is actually equal to couple-intramol = no with lambda = 0. Should that be the case? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Dallas Warren Sent: Tuesday, 22 October 2013 2:49 PM To: Discussion list for GROMACS users Subject: [gmx-users] RE: Gibbs Energy Calculation and charges I have completed the simulations using couple-intramol = yes Reminder, have a molecule that are calculating the Gibbs energy of hydration and solvation (octanol). In one topology the only difference is the atomic charges have been doubled. Considering that charges are scaled linearly with lambda, the normal charge values of dH/dl from lambda 0 to 1 obtained should reproduce that of the double charged molecule from lambda 0.5 to 1.0. Here is the mdout.mdp file from one of the simulations using couple- intramol = yes. The difference with the simulations run using couple- intramol = no is only that setting, checked using the diff command. Copy of the mdout.mdp file can be found: http://ozreef.org/stuff/gromacs/mdout.mdp Changing to couple-intrmol = yes makes things significantly worse. Here are the plots of dH/dl obtained as a function of the charge of one of the atoms, OE (calculated based on fact that at lambda = 0 fully charged, lambda = 1 no charged) http://ozreef.org/stuff/gromacs/couple-intramol.png Anyone with some insight on what is going on here? From the manual: couple-intramol: no All intra-molecular non-bonded interactions for moleculetype couple-moltype are replaced by exclusions and explicit pair interactions. In this manner the decoupled state of the molecule corresponds to the proper vacuum state without periodicity effects. yes The intra-molecular Van der Waals and Coulomb interactions are also turned on/off. This can be useful for partitioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. The 1-4 pair interactions are not turned off. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Dallas Warren Sent: Thursday, 17 October 2013 3:32 PM To: Discussion list for GROMACS users Subject: [gmx-users] RE: Gibbs Energy Calculation and charges Chris, Thank you, that appears to be the issue then. Running them again now with couple-intramol = yes Will report back once that is completed with the results. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Christopher Neale Sent: Thursday, 17 October 2013 2:15 PM To: gmx-users@gromacs.org Subject: [gmx-users] Gibbs Energy Calculation and charges Ah, I see. I guess that you are using couple-intramol = no (the default in v4.6.3 at least). That means that the intramolecular charge-charge interactions are always at full- strength (and therefore different). I would expect that normal at lambda=0 should be the same as double at lambda=0.5 only for couple-intramol = yes If you were using couple-intramol = yes already, then I am as confused as you are. Chris. -- original message -- You are correct in the first part of your statement, part that isn't correct is I expect for the same charge on the atom I expect it to give the same dH/dl value. For example, for the OE atom that I provided the graphs for ( http://ozreef.org/stuff/octanol.gif and http://ozreef.org/stuff/water.gif ) Lambda Normal 0.-0.5310 Double
Re: [gmx-users] RE: Gibbs Energy Calculation and charges
I think the grammar got a little garbled there, so I'm not sure quite what you are claiming. One important thing to remember; 1-4 interactions are treated as bonded interactions right now FOR COUPLE intramol (not for lambda dependence of the potential energy function), so whether couple-intramol is set to yes or no does not affect these interactions at all. It only affects the nonbondeds with distances greater than 1-5. At least to me, this is nonintuitive (and we're coming up with a better scheme for 5.0), but might that explain what you are getting? On Tue, Oct 29, 2013 at 9:44 PM, Dallas Warren dallas.war...@monash.edu wrote: Just want this to make another pass, just in case those in the know missed it. Using couple-intrmol = yes the resulting dH/dl plot actually looks like that at lamba = 1 it is actually equal to couple-intramol = no with lambda = 0. Should that be the case? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Dallas Warren Sent: Tuesday, 22 October 2013 2:49 PM To: Discussion list for GROMACS users Subject: [gmx-users] RE: Gibbs Energy Calculation and charges I have completed the simulations using couple-intramol = yes Reminder, have a molecule that are calculating the Gibbs energy of hydration and solvation (octanol). In one topology the only difference is the atomic charges have been doubled. Considering that charges are scaled linearly with lambda, the normal charge values of dH/dl from lambda 0 to 1 obtained should reproduce that of the double charged molecule from lambda 0.5 to 1.0. Here is the mdout.mdp file from one of the simulations using couple- intramol = yes. The difference with the simulations run using couple- intramol = no is only that setting, checked using the diff command. Copy of the mdout.mdp file can be found: http://ozreef.org/stuff/gromacs/mdout.mdp Changing to couple-intrmol = yes makes things significantly worse. Here are the plots of dH/dl obtained as a function of the charge of one of the atoms, OE (calculated based on fact that at lambda = 0 fully charged, lambda = 1 no charged) http://ozreef.org/stuff/gromacs/couple-intramol.png Anyone with some insight on what is going on here? From the manual: couple-intramol: no All intra-molecular non-bonded interactions for moleculetype couple-moltype are replaced by exclusions and explicit pair interactions. In this manner the decoupled state of the molecule corresponds to the proper vacuum state without periodicity effects. yes The intra-molecular Van der Waals and Coulomb interactions are also turned on/off. This can be useful for partitioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. The 1-4 pair interactions are not turned off. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Dallas Warren Sent: Thursday, 17 October 2013 3:32 PM To: Discussion list for GROMACS users Subject: [gmx-users] RE: Gibbs Energy Calculation and charges Chris, Thank you, that appears to be the issue then. Running them again now with couple-intramol = yes Will report back once that is completed with the results. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Christopher Neale Sent: Thursday, 17 October 2013 2:15 PM To: gmx-users@gromacs.org Subject: [gmx-users] Gibbs Energy Calculation and charges Ah, I see. I guess that you are using couple-intramol = no (the default in v4.6.3 at least). That means that the intramolecular charge-charge interactions are always at full- strength (and therefore different). I would expect that
