[gmx-users] Compute average forces along a trajectory
Dear all, I have a short simulation in implicit solvent and I want to compute the average force acting on the molecule at each frame. I tried to run the following g_traj -f traj.trr -s traj.tpr -cf -af force.xvg but I get the following error: No frames found for average force, will not write force.pdb. The .trr and .tpr files are provided as output of the md simulation. What am I doing wrong? Thanks. Simone -- -- Simone Orioli PhD Student in Statistical Mechanics of Biomolecules Dipartimento di Fisica Universita' degli Studi di Trento Via Sommarive 14, Povo (Trento) 38123, Italia Phone: +39 333 8116141 -- 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] Compute average forces along a trajectory
Dear Mark, Thanks. I did not specify that parameter, as you correctly suggested. I'm re-running the simulations and see what happens. Thanks Simone Il lun 2 apr 2018, 17:44 Mark Abraham ha scritto: > Hi, > > Probably you didn't use nstfout to save forces - use gmx check -f on your > trajectory file to see. > > Mark > > On Mon, Apr 2, 2018, 15:55 Simone Orioli wrote: > > > Dear all, > > I have a short simulation in implicit solvent and I want to compute the > > average force acting on the molecule at each frame. I tried to run the > > following > > > > g_traj -f traj.trr -s traj.tpr -cf -af force.xvg > > > > but I get the following error: > > > > No frames found for average force, will not write force.pdb. > > > > The .trr and .tpr files are provided as output of the md simulation. What > > am I doing wrong? Thanks. > > > > Simone > > -- > > > > > -- > > Simone Orioli > > PhD Student in Statistical Mechanics of Biomolecules > > > > Dipartimento di Fisica > > Universita' degli Studi di Trento > > Via Sommarive 14, Povo (Trento) > > 38123, Italia > > > > Phone: +39 333 8116141 > > -- > > 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.
Re: [gmx-users] Lowest energy structure after production MD run
Hello Neena, Hello gromacs users, > > Since the final structure obtained after production MD run is the average > structure, What do you mean by average structure? The last frame of your MD trajectory is not an average one, it's the state of your system at the final time of your simulation. how to extract out the lowest energy structure? > I'm assuming a free energy is what you're interested in. In that case you have to answer some questions before doing the actual calculation: 1) what are the relevant collective variables that define your system? 2) do you think your simulation is long enough to accurately sample the region of conformational space you're interested in? If so, you can project your trajectory on the space defined by the relevant collective variables you defined in 1), take -log of it and look for the minima of this function: this will provide an estimation of the free energy (Helmholtz in NVT ensemble, Gibbs in NPT ensemble) of your system in units of kBT. Of course you would have to check for convergence at some point, but this is a way to start. If the answer to the question is no, instead, you should consider either simulating for a longer time or using some enhanced sampling strategy > > Thank you for sharing your knowledge, > Neena > Cheers, Simone > -- > 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] Help for GROMACS best performance system
Hi, The answer to this question is very system dependent, so my suggestion is to run a benchmark simulation. If you're simulating a system in explicit solvent, the performance will remain pretty much stable in time, so you can run a very short simulation (i.e. 100ps) and check at the end of the log file how many nanoseconds per day would you simulate with a given hardware configuration. You might want to try many different hardware configurations and see which one provides the highest ns/day ratio for your system. Best, Simone Il sab 20 apr 2019, 21:09 Ali Sufali ha scritto: > Hi > > It's been a while I have started using GROMACS for my researches and now I > want to buy a system with powerful performance. > > I want to choose between these two options > Is it better to have multiple graphics card on a 12-24 core system or it is > better to have one or two graphics card on multiple systems which have > 12-24 cores ? > > > > > Ali Sufali > M.Sc. Student > University of Tehran > -- > 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] Removing periodic boundary conditions on a dimer
Hi, Have you tried the following? It usually worked for me, but I used to run simulations on old versions of Gromacs so it might be deprecated. trjconv -f system.xtc -s system.tpr -o system_nojump.xtc -pbc mol Il mar 23 apr 2019, 10:51 Nawel Mele ha scritto: > Dear Gromacs users, > > I have a dimer system with a ligand in one of the monomer. I am trying to > remove the periodic boundary conditions to visualise my simulation but > whatever steps I used the monomers don't want to be centered in the box. > I tried these steps using a custom index file corresponding to the residues > near the active site so I would center around them: > > trjconv -f system.xtc -s system.tpr -o system_nojump.xtc -pbc nojump > trjconv -f system_nojump.xtc -s system.tpr -o system_center.xtc -center > -pbc whole -ur compact -n index_file_center.ndx > > I am confused on the steps I should be using with these kind of system, do > you have any suggestions ? > > Many thanks, > > Regards > > -- > > Dr Nawel Mele, > T: +33 (0) 634443794 (Fr) > > +44 (0) 7704331840 (UK) > -- > 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] SASA calculation for one replica in REMD
Hi, I don't know if sasa calculations are implemented in gromacs. But if you know a little bit of Python you can use MDTraj for that: http://mdtraj.org/latest/examples/solvent-accessible-surface-area.html or also Pymol: https://pymolwiki.org/index.php/Get_Area Cheers, Simone Il mar 23 apr 2019, 11:07 Shan Jayasinghe ha scritto: > Dear Gromacs Users, > > I did replica exchange molecular dynamics simulation which contains 25 > replicas. Now I want to calculate the solvent accessible surface area of > the surfactant (the first replica in my REMD) I used in my simulation at > 298 K. How can I do that? > > Can anyone help me? > > Thank you. > -- > 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.
[gmx-users] Visualizing hexamer with solvent
Hello everyone, I'm simulating a hexamer and I would like to visualize it together with solvent (to see if the core of the complex is getting hydrated). However, all my attempts with trjconv have been unsuccessful. I know that in principle one should do the following gmx trjconv -f md.trr -s md.tpr -pbc mol -ur compact -center -o centered.xtc but I'm not sure which group I have to choose for centering. I read online that it should be only one of the chains, but if I try to pass an index file with -n, trjconv automatically assumes I want to use the same indices for both centering and output, which is not the case. What am I doing wrong? Thank you for your help! Simone -- 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.
