Re: [gmx-users] GROMACS 4.6.4 is released
Will a simulation from 4.6.1 continue running fine if I upgrade to 4.6.4? Hi GROMACS users, GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and some noteworthy simulation performance enhancements (particularly with GPUs!). We encourage all users to upgrade their installations from earlier 4.6-era releases. You can find the code, manual, release notes, installation instructions and test suite at the links below. Note that some tests have been added, and the manual has changed only in chapter 7 and appendix D. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.4.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.4.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.4 http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.4.tar.gz Happy simulating! The GROMACS team -- 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] Energy minimization has stopped....
What does your curve look like? What parameters are you using in the mdp? How big is your system and what kind of molecules are in there? Providing this kind of information would help people work out what the problem is. Then again it may be ok that the minimisation has converged without reaching the Fmax cutoff. 2 is a large number of steps. Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 gcq#322: The Feeling of Power was Intoxicating, Magic (Frida Hyvonen) -- Kalyanashis Jana email: kalyan.chem...@gmail.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
Re: [gmx-users] Lysozyme in Water at different pH and Ionic strength
I notice that both papers mention modifications to GROMACS and cite the following: http://www.ncbi.nlm.nih.gov/pubmed/16471903 Following up on Justin's reply I just want to add that, not only is it possible, as it has been done before. For instance: http://www.ncbi.nlm.nih.gov/pubmed/18214978 http://www.ncbi.nlm.nih.gov/pubmed/22072522 Luís Filipe ITQB-UNL, Portugal 2013/11/1 Justin Lemkul jalem...@vt.edu On 11/1/13 8:39 AM, xiao wrote: It is impossible. But you can add proton to the acidic amino acid. It's certainly not impossible. There are constant-pH methods that exist; the list archive contains many posts on this topic, and more information can be found at: http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulationhttp://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Whether or not you can easily accomplish such simulations in Gromacs is another matter. Standard MD does not allow for dynamic protonation states, so the closest you can get without running more advanced MD is to use fixed protonation states, assigned by pdb2gmx, that are indicative of the most prevalent state of the residues at a given pH value. Changing ionic strength is trivial; that's what genion -conc is for. -Justin At 2013-11-01 20:36:41,Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs users, Just was wondering if it is possible to protein solution let say Lysozyme in Water example of Justin tutorial at different pH and ionic strengths, if so how? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 91
I think ProDy can do this. It is a python module for analysis of structures that can be downloaded from http://www.csb.pitt.edu/ProDy/ I'm not sure it can read xtc but you can probably use it after converting trajectories to pdb. On 10/30/13 11:26 AM, Knapp Bernhard wrote: Hi users, I was wondering if there is an easy and quick way to get a frame-wise binding energy between 2 groups of chains (chain ABC vs DE) in an existing trajectory. This is not indented to be an actual binding free energy approach but rather a rough indicator if the binding between two chains increases or decreases during simulation time. This should work like a protein/protein docking scoring function which assigns binding scores to single conformations. Is there a direct approach on an existing xtc (even if water was removed and not all steps were written)? Maybe like g_hbond but in addition with terms like Gvdw, Gdeformation, Ghydrophobic etc. Alternatively (and probably much more time and resource consuming), would it be possible to obtain this by the rerun option of mdrun (adjusted energy monitoring groups (the original setup was energygrps = proteinSOL))? Using energygrps is the closest you'll get without modifying the code. You'll get decomposed short-range nonbonded terms, which can perhaps provide some indicator of the strength of the interaction between the two entities. -Justin Hmm ok if Gromacs does not provide something like this then I ask the question a little bit different: Does someone know a pure scoring function for protein/protein interaction? It should not be a complete docking program but rather something which can simply evaluate given conformations (coming from an MD trajectory) ... and it should also not be a webserver (like ClusPro) but a downloadable binary because I want to test a quite high amount of conformations. Something like XSCORE [J Comp Aid Des, 16: 11-26. 2002] but instead of ligand/protein for protein/protein interactions. Cheers, Bernhard -- 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] Lysozime in Water
Yes, I would use the same command to continue the simulation after stopping with the addition of -cpi Every time a .cpt is made, the previous one is renamed _prev.cpt so that you can still get it in case something happened in between the two. Normally I would use the .cpt but if that doesn't work then try the _prev.cpt I think someone already replied to this question but I guess that didn't help enough. Hopefully this reply does. Dear Gromacs users Hello, I use gromacs version 4.5.5. I have started with Lysozime in water simulation. (Justin tutorials) The md part of simulation was terminated. Now I want to continue the simulation from the interruption point. Is this command line correct? mdrun -deffnm md_0_1 -smd_0_1.tpr -cpi md_0_1.tpr.cpt??? I am not sure whether to use only *-cpi md_0_1.tpr.cpt* with mdrun command or both *.tpr* and .*cpt* files??? another question is that whether continuing the simulation should be done via file *md_0_1.tpr.cpt* or *md_0_1.tpr_prev.cpt* ? and what in the difference between them? Thanks in advance Regards Negar -- 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] mdrun cpt
No this isn't a problem. You can use job names under the -hold_jid flag. As long as you change the job name in the submit script between submissions this isn't a problem. You could have a submit script for job 4 with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and -hold_jid md_job4 for the next job. Then you can submit job 5 as soon as you have made this change which will be within seconds of submitting job 4. 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. Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. 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.comwrote: 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 Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
Re: [gmx-users] mdrun cpt
You're welcome On 28 Oct 2013, at 20:03, Pavan Ghatty pavan.grom...@gmail.com wrote: Aah yes of course. Thanks James. On Mon, Oct 28, 2013 at 3:16 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: No this isn't a problem. You can use job names under the -hold_jid flag. As long as you change the job name in the submit script between submissions this isn't a problem. You could have a submit script for job 4 with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and -hold_jid md_job4 for the next job. Then you can submit job 5 as soon as you have made this change which will be within seconds of submitting job 4. 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. Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. 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.comwrote: 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 Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] nstcalclr bug?
I think nstcalclr would only do something if you have longer range interactions to calculate (lr means longer than rlist). Therefore something has be longer than rlist for this to happen. Hi there, I am using gromacs-4.6.1 with this mdp file: integrator= md; leap-frog integrator nsteps= 300 ; 6.0 ns dt= 0.002 ; 2 fs nstxout = 0 ; save coordinates every 10 ps nstvout = 0 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog= 5000 ; update log file every 5 ps nstcalcenergy = 100 ; nstxtcout = 5000 ; xtc every 10 ps xtc_precision = 100 continuation = yes ; Restarting constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ns_type = grid ; search neighboring grid cells nstlist = 20; 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) nstcalclr= 10 cutoff-scheme = Group vdwtype = Cut-off vdw-modifier = Potential-shift coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing= 0.16 ; grid spacing for FFT coulomb-modifier = Potential-shift tcoupl= V-rescale ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K energygrps = complex Water; group(s) to write to energy file pcoupl= Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype= isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord_scaling = com pbc = xyz ; 3-D PBC DispCorr = EnerPres ; account for cut-off vdW scheme gen_vel = no; Velocity generation is off gen-seed= 128742 ; number of steps for center of mass motion removal nstcomm = 1000 the mdout.mdp file says nstcalclr = 10, but gmxdump of the tpr file says nstcalclr = 0. If I set rvdw = 1.4 ( rlist), gmxdump of the file tpr is now correct to nstcalclr = 10. I have double checked the manual but I couldn't find the reason of this behaviour. is this a bug or am I doing wrong somewhere?? thanks for any helps and Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 -- 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] a new GROMACS simulation tool
Please could I have an account too. Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- 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] pbc problem
I usually use -pbc nojump for my protein simulations and this works every time. Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water molecules in top leaflet. For both positions, I did energy minimization successfully with following mdp file. -- ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions --- After energy minimization, I saw obtained file (em.gro) by VMD. All things were true and intact. For both positions, I did equilibration in NPT ensemble with following mdp file. --- ; Run parameters integrator= md; leap-frog integrator nsteps= 25; 2 * 50 = 1000 ps (1 ns) dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstxtcout = 100; xtc compressed trajectory output every 2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps energygrps = CHOL DOPC drg SOL ; Bond parameters continuation= no; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 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= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; More accurate thermostat tc-grps= CHOL_DOPCdrg SOL; three coupling groups - more accurate tau_t= 0.50.5 0.5 ; time constant, in ps ref_t= 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 5.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 323; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = CHOL_DOPC_drg SOL ; Scale COM of reference coordinates refcoord_scaling = com --- For 2 positions, I chechked tempreture and pressure fluctuation and box dimention during equilibration. All things were good. When I saw trajectory by VMD (npt.gro and npt xtc), I had pbc problem (some atoms leave box and enter the box in opposit direction). For position (a): I corrected pbc problem by
Re: [gmx-users] Molecular dynamics with LEGO?
Hi Tsjerk, In my opinion, we don't need to develop LEGO specifically for this - something already exists, which I played with in school. The molymod pieces (http://www.molymod.com/) already include bendy pieces, which are the next step on the lego website you advertise. Best wishes James Hi :) Apologies if this seems inappropriate, but I would like to ask as many people as I can to give support for the molecular modeling LEGO project at http://lego.cuusoo.com/ideas/view/51273. With 10 000 votes, LEGO will consider producing the bricks required for such models, and we can add cool a way of modeling to our toolbox. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Hai friends (balu)
I suppose there would also be a way of passing do_dssp output on to make_ndx then you could use the index with g_hbond to count hbonds in each secondary structure element. Best wishes James If the goal is to simply count the secondary structure, pass the dssp output file through grep __ dssp_output.xpm | wc Fill in the dssp code for each secondary structure in the underline separately. Grep would extract all characters that fit that pattern and wc would count it. Hope that helps. Ali -- 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
