Re: [gmx-users] disulfide bridges
Oh thank you so much, I did not know it was a reference value. Given a range of values might exist in one system I'm guessing minimization would be the only way to deal with such a situation. Best, Miro On Sat, May 2, 2020 at 9:53 PM Justin Lemkul wrote: > > > On 5/2/20 6:54 AM, Miro Astore wrote: > > Hi all, > > > > I'm trying to make a protein with a fair few disulfide bridges and I > > couldn't get it to work. I chose -ss yes and increased the minimum > distance > > in specbonds.dat but it doesn't seem to want to let me see all possible > > pariings. > > specbond.dat does not set minimum distances. It sets a reference value, > and a bond is only assigned if the distance in the coordinate file is > within 10% of that reference. So if you were, for example, to increase > the value from 0.2 nm (conventional) to 0.3 nm, you'll miss the > disulfides that should be formed because the new reference range is 0.27 > - 0.33 nm and anything between 0.18 - 0.22 nm will not be assigned a > disulfide linkage. > > > Any way I can nudge it in the right direction without performing a > > minimisation with restraints? > > Depends on the range of distances in your structure, but this is often > what you have to do. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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] disulfide bridges
Hi all, I'm trying to make a protein with a fair few disulfide bridges and I couldn't get it to work. I chose -ss yes and increased the minimum distance in specbonds.dat but it doesn't seem to want to let me see all possible pariings. Any way I can nudge it in the right direction without performing a minimisation with restraints? Best, Miro -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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] debugging
Hi all, I am interested in how Gromacs works at the back end but I don't have much C experience so this might be silly. I have noticed that one of my systems that includes virtual sites parses fine through grompp in gromacs 2019.1 and 3 but fails in 2020.1 with a segmentation fault. 21169 Segmentation fault (core dumped) I'd like to try and debug this further. Should I try and go after this myself? -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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] semiisotropic pressure coupling.
Incredible thank you. On Wed., 15 Apr. 2020, 8:46 pm Justin Lemkul, wrote: > > > On 4/14/20 10:12 PM, Miro Astore wrote: > > Hello all, > > > > I am working with a rather large membrane bound protein. I was getting > > an issue awhile ago where if the protein moved to the edge of the box > > the box would elongate in the z direction. I fixed this in the short > > term by setting my xy compressibility to 0 in my production mdp file > > pcoupl = Parrinello-Rahman > > pcoupltype = semiisotropic > > tau_p = 5.0 > > > > compressibility = 0 4.5e-5 > > ref_p = 1.0 1.0 > > compressibility = 0 4.5e-5 > > ref_p = 1.0 1.0 > > > > I have a few questions, why was it blowing up in the first place? I > > This was due to a CHARMM-specific bug in which CMAP forces were not > correctly calculated when two atoms were in different periodic images: > > http://manual.gromacs.org/current/release-notes/2019/2019.4.html#fix-incorrect-pressure-when-atoms-in-cmap-cross-a-box-boundary > > It was fixed in version 2019.4. > > Update your GROMACS version and you don't have to try playing any tricks > like zero compressibility. > > -Justin > > > would guess its to do with how the pressure is being calculated when > > this large 'vacuum' is being created in the solvent when the protein > > wraps around since my tc_grps is Protein non-Protein. The fact the > > problem only occurs when the protein wraps seems to indicate this sort > > of artifact, I can get into the hundreds of nano seconds before the > > protein drifts if I'm lucky, this is all after a well equilibrated > > system. > > > > I could fix the protein in the center of the box but I fear that might > > produce artifacts and I suspect there is a better way. > > > > I want to start studying how this protein interacts with the lipids > > and fixing the xy box size is not conducive to this so I'm wondering > > how I can let the lipids fluctuate while still maintaining sensible > > system behavior. > > > > Thank you for your time, > > > > Best, Miro > > > > mdp file can be found at > > > https://docs.google.com/document/d/16vsS4OOco9U3bUkarzSduN2OXohnBVVLedwLJanUi4w/edit?usp=sharing > > -- > > Miro A. Astore (he/him) > > PhD Candidate | Computational Biophysics > > Office 434 A28 School of Physics > > University of Sydney > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] semiisotropic pressure coupling.
Hello all, I am working with a rather large membrane bound protein. I was getting an issue awhile ago where if the protein moved to the edge of the box the box would elongate in the z direction. I fixed this in the short term by setting my xy compressibility to 0 in my production mdp file pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 0 4.5e-5 ref_p = 1.0 1.0 compressibility = 0 4.5e-5 ref_p = 1.0 1.0 I have a few questions, why was it blowing up in the first place? I would guess its to do with how the pressure is being calculated when this large 'vacuum' is being created in the solvent when the protein wraps around since my tc_grps is Protein non-Protein. The fact the problem only occurs when the protein wraps seems to indicate this sort of artifact, I can get into the hundreds of nano seconds before the protein drifts if I'm lucky, this is all after a well equilibrated system. I could fix the protein in the center of the box but I fear that might produce artifacts and I suspect there is a better way. I want to start studying how this protein interacts with the lipids and fixing the xy box size is not conducive to this so I'm wondering how I can let the lipids fluctuate while still maintaining sensible system behavior. Thank you for your time, Best, Miro mdp file can be found at https://docs.google.com/document/d/16vsS4OOco9U3bUkarzSduN2OXohnBVVLedwLJanUi4w/edit?usp=sharing -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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] replica exchange simulations performance issues.
I got up to 25-26 ns/day with my 4 replica system (same logic scaled up to 73 replicas) which I think is reasonable. Could I do better? mpirun -np 48 gmx_mpi mdrun -ntomp 1 -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 I have tried following the manual but I don't think i'm going it right I keep getting errors. If you have a minute to suggest how I could do this I would appreciate that. log file accounting: R E A L C Y C L E A N D T I M E A C C O U N T I N G On 12 MPI ranks Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % - Domain decomp. 12 1 26702 251.490 8731.137 1.5 DD comm. load 12 1 25740 1.210 42.003 0.0 DD comm. bounds 12 1 26396 9.627 334.238 0.1 Neighbor search 12 1 25862 283.564 9844.652 1.7 Launch GPU ops. 12 1 5004002 343.309 11918.867 2.0 Comm. coord. 12 1 2476139 508.526 17654.811 3.0 Force 12 1 2502001 419.341 14558.495 2.5 Wait + Comm. F 12 1 2502001 347.752 12073.100 2.1 PME mesh 12 1 2502001 11721.893 406955.915 69.2 Wait Bonded GPU 12 1 2503 0.008 0.285 0.0 Wait GPU NB nonloc. 12 1 2502001 48.918 1698.317 0.3 Wait GPU NB local 12 1 2502001 19.475 676.141 0.1 NB X/F buffer ops. 12 1 9956280 753.489 26159.337 4.5 Write traj. 12 1 519 1.078 37.427 0.0 Update 12 1 2502001 434.272 15076.886 2.6 Constraints 12 1 2502001 701.800 24364.800 4.1 Comm. energies 12 1 125942 36.574 1269.776 0.2 Rest 1047.855 36378.988 6.2 - Total 16930.182 587775.176 100.0 - Breakdown of PME mesh computation - PME redist. X/F 12 1 5004002 1650.247 57292.604 9.7 PME spread 12 1 2502001 4133.126 143492.183 24.4 PME gather 12 1 2502001 2303.327 79965.968 13.6 PME 3D-FFT 12 1 5004002 2119.410 73580.828 12.5 PME 3D-FFT Comm. 12 1 5004002 918.318 31881.804 5.4 PME solve Elec 12 1 2502001 584.446 20290.548 3.5 - Best, Miro On Tue, Mar 31, 2020 at 9:58 AM Szilárd Páll wrote: > > On Sun, Mar 29, 2020 at 3:56 AM Miro Astore wrote: > > > Hi everybody. I've been experimenting with REMD for my system running > > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > > because this is a complicated system with many DOF I'm open to being > > told this is all a silly idea). > > > > It is a bad idea, you should have at least 1 physical core per replica and > with a large system ideally more. > However, if you are going for high efficiency (aggregate ns/day per phyical > node), always put at least 2 replicas per GPU. > > > > > > My run configuration is > > mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 > > -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 > > > > the best I can squeeze out of this is 9ns/day. In a non-replica > > simulation I can hit 50ns/day with a single GPU and 12 cores. > > > > That is abnormal and indicates that: > - either something is wrong with the hardware mapping / assignment in your > run or; do use simply "-pin on" and let mdrun manage threads pinning (that > map-by-numa is certainly not optimal); also I advise against tweaking the > thread count and using weird numbers like 11 (just use quarter); > - your exchange overhead is very high (check the communication cost in the > log) > > If you share some log files of a standalone and a replex run, we can advise > where the performance loss comes from. > > Cheers, > -- > Szilárd > > Looking at my accounting, for a single replica 52% of time is being > > spent on the "Force" category with 92% of my Mflops going into NxN > > Ewald Elec. + LJ [F] > > > > > I'm wondering what I could do to reduce this bottle neck if anything. > > > > Thank you. > > -- > > Miro A. Astore (he/him) > > PhD Candidate | Computational Biophysics > > Office 434 A28 School of Physics > > University of Sydney > > -- > > 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.
Re: [gmx-users] replica exchange simulations performance issues.
After much experimentation I managed to run mpirun -np 48 gmx_mpi mdrun -ntomp 1 -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 on a single node at 27 ns/day. This scaled up for 73 replicas on my 190 000 atom system ( using the same logic -np num_sims*12) on our gadi cluster in australia. I will soon see if i can get away with fewer replicas. Thanks for your help. Miro On Sun, Mar 29, 2020 at 9:04 PM Benson Muite wrote: > > > On Sun, Mar 29, 2020, at 4:55 AM, Miro Astore wrote: > > Hi everybody. I've been experimenting with REMD for my system running > > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > > because this is a complicated system with many DOF I'm open to being > > told this is all a silly idea). > > > > My run configuration is > > mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 > > -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 > > > > the best I can squeeze out of this is 9ns/day. In a non-replica > > simulation I can hit 50ns/day with a single GPU and 12 cores. > > What happens for a small number of replicas? > > > > > Looking at my accounting, for a single replica 52% of time is being > > spent on the "Force" category with 92% of my Mflops going into NxN > > Ewald Elec. + LJ [F] > > > > I'm wondering what I could do to reduce this bottle neck if anything. > > Do you have access to more hardware? There area number of HPC centers in > Australia. > > > > > Thank you. > > -- > > Miro A. Astore (he/him) > > PhD Candidate | Computational Biophysics > > Office 434 A28 School of Physics > > University of Sydney > > -- > > 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. -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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] replica exchange simulations performance issues.
correction: 99.3% is going into NxN Ewald Elec. + LJ [F] On Sun, Mar 29, 2020 at 12:55 PM Miro Astore wrote: > > Hi everybody. I've been experimenting with REMD for my system running > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > because this is a complicated system with many DOF I'm open to being > told this is all a silly idea). > > My run configuration is > mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 > -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 > > the best I can squeeze out of this is 9ns/day. In a non-replica > simulation I can hit 50ns/day with a single GPU and 12 cores. > > Looking at my accounting, for a single replica 52% of time is being > spent on the "Force" category with 92% of my Mflops going into NxN > Ewald Elec. + LJ [F] > > I'm wondering what I could do to reduce this bottle neck if anything. > > Thank you. > -- > Miro A. Astore (he/him) > PhD Candidate | Computational Biophysics > Office 434 A28 School of Physics > University of Sydney -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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] replica exchange simulations performance issues.
Hi everybody. I've been experimenting with REMD for my system running on 48 cores with 4 gpus (I will need to scale up to 73 replicas because this is a complicated system with many DOF I'm open to being told this is all a silly idea). My run configuration is mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 the best I can squeeze out of this is 9ns/day. In a non-replica simulation I can hit 50ns/day with a single GPU and 12 cores. Looking at my accounting, for a single replica 52% of time is being spent on the "Force" category with 92% of my Mflops going into NxN Ewald Elec. + LJ [F] I'm wondering what I could do to reduce this bottle neck if anything. Thank you. -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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] Script for looping n simulations
I have something like this on my github. https://github.com/Miro-Astore/gromacs_scripts/tree/master/pbs_files/gadi File is memb0.pbs let me know if you have any questions. On Sat., 15 Feb. 2020, 8:45 am Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hello gromacs users, > > I was wondering how to write a script to repeat a simulation > (equilibration and production) n times, with each cycle starting with > structure from the end of previous cycle. > > Many thanks, > Neena > -- > 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] misunderstanding comm-grps
Oh thank you very much I think I got confused looking at older documentation. What sort of artefacts get created by using comm-grps = Protein non-Protein? On Wed, Feb 5, 2020 at 11:14 PM Justin Lemkul wrote: > > > > On 2/3/20 7:33 PM, Miro Astore wrote: > > Hi everyone, > > > > I have tried using comm_grps to try and remove center of mass motion > > from my system. > > > > I used the following configuration > > > > comm_grps = non-Protein Protein > > nstcomm = 100 > > comm_mode = linear > > comm_grps = non-Protein Protein > > Don't do this. Multiple COM motion removal groups are only appropriate > in layered systems that have different diffusion behavior. > > > >refcoord_scaling= com > > > > But I still get considerable drift in my protein. Am I > > misunderstanding what comm is actually doing and I should use the > > pulling code if I want my protein to stay in the center of the box? > > Dallas covered this nicely. The algorithm does not (and is not intended > to) prevent diffusion. It subtracts erroneous contributions to the > kinetic energy in the system. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] misunderstanding comm-grps
Hi everyone, I have tried using comm_grps to try and remove center of mass motion from my system. I used the following configuration comm_grps = non-Protein Protein nstcomm = 100 comm_mode = linear comm_grps = non-Protein Protein refcoord_scaling= com But I still get considerable drift in my protein. Am I misunderstanding what comm is actually doing and I should use the pulling code if I want my protein to stay in the center of the box? Best, Miro -- 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] Charmm to Gromacs itps
Would topotools in vmd not work in this context? I haven't used it but read about it recently and it would seem this is the use case. Of course you also need parameters. Wondering. Best, Miro Le sam. 1 févr. 2020 à 00:55, Justin Lemkul a écrit : > > > On 1/31/20 8:25 AM, atb files wrote: > > > > > > > > The files are given on the following server: > https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated > systems using NAMD. > > If the individual topologies are not available anywhere, just a PSF, > then you will have to write your own converter program to transform the > PSF into GROMACS .top format. PSF is very verbose so this should be > straightforward. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] constant x-y plane area for membrane simulations.
Hello all, I'm just wondering if gromacs supports constant x-y plane area for npt simulations like NAMD does. Best, Miro -- 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] trjcat and trjconv performance
Hello all. I need to use trjcat and trjconv often and I am wondering if there is any way to speed up these utilities. They seem quite slow at the moment compared to the catdcd binary in the vmd distribution. Best, Miro -- 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] learning gromacs
Hi, I'm new to gromacs myself. Your best bet if you're new to Molecular dynamics is to do some tutorials and read best practices to try and understand what the computer is actually doing and why. http://www.mdtutorials.com/gmx/ I would recommend starting with the lysozyme in water tutorial as it is the simplest and then working through the ones that are relevant to your work. https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0 - best practice guide to help you better understand how not to waste computer time running meaningless simulations. Just because a simulation runs does not mean it is correct or useful. other handy resources. the documentation for the software. http://manual.gromacs.org/ also googling any error messages you find will usually bring up a research gate post or a message from this mailing list where someone has had the same problem. Hope this helps you getting started. Good luck. Best, Miro On Mon, Jan 27, 2020 at 6:24 PM Somdatta Chaudhari wrote: > Want to learn gromacs...plz help me out in this regards > > -- > Somdatta Y. Chaudhari > M.Pharm(Pharma.Chem) > Lecturer > Dept- Pharma.Chem > Modern College of Pharmacy, > Nigdi, Pune. (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] top2psf license
I have contacted the author Marc Baaden and he has told me that the script should be distributed under BDS-3 clause version. Please if you do modify or distribute this script make sure you copy the license text in the header. He's also asked me to share that unity Mol can determine topology and secondary structures without the need for such a script, directly reading itp files. Even being able to determine secondary structures from martini. https://twitter.com/Matth_Chavent/status/1145727900286693376 Best, Miro Le mer. 22 janv. 2020 à 20:07, Miro Astore a écrit : > Does anyone know what the license is for the top2psf.pl script. > > I'd like to modify and distribute it if possible. > > Best, Miro. > > -- 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] top2psf license
Does anyone know what the license is for the top2psf.pl script. I'd like to modify and distribute it if possible. Best, Miro. -- 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] Loading topology into vmd
This is very helpful thank you. I think I can use this. I will also ask the vmd mail list. Best, Miro Le mer. 15 janv. 2020 à 19:35, Alessandra Villa < alessandra.villa.bio...@gmail.com> a écrit : > Hi, > One of the criteria that VMD uses to define bond is distance criteria. When > you source your gro file, this criteria is applied. > One way one, I have used is to not visualize undesired bonds, is the > following: > delete the undesired bonds, save the vmd setting (*.vmd file), load the > setting before any of the following visualizations. > That is not the most elegant way, but it works in my case. > For more elegant ways, you could ask to VMD maillist. > Best regards > Alessandra > > > On Tue, Jan 14, 2020 at 8:59 PM Miro Astore wrote: > > > Hi kenny, thanks for getting back to me. > > > > I use something similar to what you've suggested to deal with periodic > > boundary conditions. My current issue is that vmd will place a bond > between > > two atoms that are close together in the first frame of the visualization > > even if those atoms aren't linked in the topology. The fake bonds are > then > > kept throughout the visualization . That is, when I load just a gro and a > > trr. > > > > A psf file would fix this situation but my efforts to recreate a whole > one > > from my complex system using top2psf.pl hasn't borne much fruit. > > > > Just wondering what other people have tried. > > > > Best, Miro > > > > Le mer. 15 janv. 2020 à 02:20, Kenny Goossens < > goossens_ke...@hotmail.com> > > a écrit : > > > > > Hi, > > > > > > I'm not sure what you mean by "bonds that aren't in the simulation", > but > > > from my experience, converting your .gro file with gmx trjconv using > the > > > -pbc mol and -ur compact options usually gives a clean visualisation. > If > > > necessary, you can also use the -center option to center a specific > > > structure/residue in the box. You can have the output written in the > .gro > > > file format, or convert to anything more convenient. > > > > > > With kind regards, > > > __ > > > Kenneth Goossens, PhD student > > > Laboratory of Medicinal Chemistry (Building A - Room 2.13) > > > University of Antwerp - Campus Drie Eiken > > > Universiteitsplein 1 > > > B-2610 Wilrijk > > > Belgium > > > > > > > > > > > > > > > Van: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> namens Miro Astore > < > > > miro.ast...@gmail.com> > > > Verzonden: dinsdag 14 januari 2020 3:48 > > > Aan: gromacs.org_gmx-users@maillist.sys.kth.se < > > > gromacs.org_gmx-users@maillist.sys.kth.se> > > > Onderwerp: [gmx-users] Loading topology into vmd > > > > > > Hello all, > > > > > > I'm just wondering how people load topologies for systems simulated in > > > gromacs into vmd. It is very annoying to have bonds that aren't in the > > > simulation placed in the visualisation. I'm wondering if anyone has a > > > solution that is easier than simply creating a psf file of the .gro > > system > > > as this can be time consuming for systems with strange geometries. > > > > > > Best, Miro > > > -- > > > 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_L
Re: [gmx-users] Loading topology into vmd
Hi kenny, thanks for getting back to me. I use something similar to what you've suggested to deal with periodic boundary conditions. My current issue is that vmd will place a bond between two atoms that are close together in the first frame of the visualization even if those atoms aren't linked in the topology. The fake bonds are then kept throughout the visualization . That is, when I load just a gro and a trr. A psf file would fix this situation but my efforts to recreate a whole one from my complex system using top2psf.pl hasn't borne much fruit. Just wondering what other people have tried. Best, Miro Le mer. 15 janv. 2020 à 02:20, Kenny Goossens a écrit : > Hi, > > I'm not sure what you mean by "bonds that aren't in the simulation", but > from my experience, converting your .gro file with gmx trjconv using the > -pbc mol and -ur compact options usually gives a clean visualisation. If > necessary, you can also use the -center option to center a specific > structure/residue in the box. You can have the output written in the .gro > file format, or convert to anything more convenient. > > With kind regards, > __ > Kenneth Goossens, PhD student > Laboratory of Medicinal Chemistry (Building A - Room 2.13) > University of Antwerp - Campus Drie Eiken > Universiteitsplein 1 > B-2610 Wilrijk > Belgium > > > > > Van: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> namens Miro Astore < > miro.ast...@gmail.com> > Verzonden: dinsdag 14 januari 2020 3:48 > Aan: gromacs.org_gmx-users@maillist.sys.kth.se < > gromacs.org_gmx-users@maillist.sys.kth.se> > Onderwerp: [gmx-users] Loading topology into vmd > > Hello all, > > I'm just wondering how people load topologies for systems simulated in > gromacs into vmd. It is very annoying to have bonds that aren't in the > simulation placed in the visualisation. I'm wondering if anyone has a > solution that is easier than simply creating a psf file of the .gro system > as this can be time consuming for systems with strange geometries. > > Best, Miro > -- > 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.
[gmx-users] Loading topology into vmd
Hello all, I'm just wondering how people load topologies for systems simulated in gromacs into vmd. It is very annoying to have bonds that aren't in the simulation placed in the visualisation. I'm wondering if anyone has a solution that is easier than simply creating a psf file of the .gro system as this can be time consuming for systems with strange geometries. Best, Miro -- 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] conveniently placing restraints on a subset of a molecule
Hello, I am new to the gromacs work flow, I come from using NAMD. An example of what I want to do is place harmonic restraints on a subset of a molecule, for example all of the CA atoms in a protein backbone. I have found the genrestr function which I would have expected would do the trick. However, as stated in the documentation the indexes won't reflect those within the molecule. I'm wondering if there is a simple way to do what I want using the gromacs work flow that doesn't include manually editing the itp files. Best, Miro. -- 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.
