Re: [gmx-users] Bilayer exploding with semiisotropic coupling
Hello, please upload the log file from the run, as well as the command you used to run the simulation and your system specs (processor, whether you are using GPUs). Then we can see what is wrong here. Thanks in advance. Cheers Paul On Sat, 4 Jan 2020, 21:14 Kevin Boyd, wrote: > Hi, > > Can you share more information? Please upload your starting configuration > and a log file. > > On Fri, Jan 3, 2020 at 10:29 AM Namit Chaudhary > wrote: > > > Hi, > > > > Sorry. I didn't realize that attachments aren't uploaded. Below is a link > > for the files mentioned in the original mail. > > > > > https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing > > > > Namit > > > > On Fri, Jan 3, 2020 at 1:12 PM Namit Chaudhary > > wrote: > > > > > Hi all, > > > > > > I am trying to simulate a coarse grain system containing DPPC (10%), > > > Cholesterol (40%) and a custom lipid that's synthesized by our lab > (50%, > > > topology and martini mapping attached). Our lab uses these molecules > to > > > formulate lipid nanoparticles and deliver RNA therapeutics. I am trying > > to > > > understand the structure of these nanoparticles. I tried modelling them > > as > > > a bilayer but the system seems to be exploding in the z - direction > > during > > > the production run if I use semiisotropic or anisotropic pressure > > coupling > > > (isotropic coupling seems to work). Below is the md.mdp file that I am > > > using. > > > > > > integrator = md > > > dt = 0.01 > > > nsteps = 800 > > > nstcomm = 100 > > > comm-grps= LIPIDS SOL > > > > > > > > > nstxout = 0 > > > nstvout = 0 > > > nstfout = 0 > > > nstlog = 1000 ; Output frequency for energies to log > > > file > > > nstenergy= 100 ; Output frequency for energies to > > energy > > > file > > > nstxtcout= 1000 ; Output frequency for .xtc file > > > xtc_precision= 100 > > > xtc-grps = > > > energygrps = > > > > > > > > > nstlist = 10 > > > ns_type = grid > > > pbc = xyz > > > rlist= 1.1 > > > > > > coulombtype = reaction_field ;Reaction_field (for use > with > > > Verlet-pairlist) ;PME (especially with polarizable water) > > > rcoulomb_switch = 0.0 > > > rcoulomb = 1.1 > > > epsilon_r= 15 ; 2.5 (with polarizable water) > > > vdw_type = cutoff ;cutoff (for use with > Verlet-pairlist) > > > > > > rvdw_switch = 0.9 > > > rvdw = 1.1 ;1.1 (for use with Verlet-pairlist) > > > > > > cutoff-scheme= verlet > > > > > > tcoupl = v-rescale > > > tc-grps = LIPIDS SOL > > > tau_t = 1.0 1.0 > > > ref_t = 298 298 > > > Pcoupl = parrinello-rahman > > > Pcoupltype= semiisotropic > > > tau_p = 12.0 > > > compressibility = 3e-4 3e-4 ; 3e-4 > > > ref_p = 1.0 1.0 ; 1.0 1.0 > > > > > > gen_vel= yes > > > gen_temp = 298 > > > gen_seed = 473529 > > > > > > constraints= none > > > constraint_algorithm = Lincs > > > continuation = no > > > lincs_order= 4 > > > lincs_warnangle= 30 > > > > > > Is there something that I can change in my mdp file? Or is there > > something > > > wrong with the lipid itself? > > > > > > > > > Thank you > > > Namit > > > > > > > > > -- > > *Namit Chaudhary* > > Chemical Engineering | Carnegie Mellon University > > M: 724-506-0693 | E: nchau...@andrew.cmu.edu > > -- > > 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
Re: [gmx-users] Bilayer exploding with semiisotropic coupling
Hi, Can you share more information? Please upload your starting configuration and a log file. On Fri, Jan 3, 2020 at 10:29 AM Namit Chaudhary wrote: > Hi, > > Sorry. I didn't realize that attachments aren't uploaded. Below is a link > for the files mentioned in the original mail. > > https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing > > Namit > > On Fri, Jan 3, 2020 at 1:12 PM Namit Chaudhary > wrote: > > > Hi all, > > > > I am trying to simulate a coarse grain system containing DPPC (10%), > > Cholesterol (40%) and a custom lipid that's synthesized by our lab (50%, > > topology and martini mapping attached). Our lab uses these molecules to > > formulate lipid nanoparticles and deliver RNA therapeutics. I am trying > to > > understand the structure of these nanoparticles. I tried modelling them > as > > a bilayer but the system seems to be exploding in the z - direction > during > > the production run if I use semiisotropic or anisotropic pressure > coupling > > (isotropic coupling seems to work). Below is the md.mdp file that I am > > using. > > > > integrator = md > > dt = 0.01 > > nsteps = 800 > > nstcomm = 100 > > comm-grps= LIPIDS SOL > > > > > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > nstlog = 1000 ; Output frequency for energies to log > > file > > nstenergy= 100 ; Output frequency for energies to > energy > > file > > nstxtcout= 1000 ; Output frequency for .xtc file > > xtc_precision= 100 > > xtc-grps = > > energygrps = > > > > > > nstlist = 10 > > ns_type = grid > > pbc = xyz > > rlist= 1.1 > > > > coulombtype = reaction_field ;Reaction_field (for use with > > Verlet-pairlist) ;PME (especially with polarizable water) > > rcoulomb_switch = 0.0 > > rcoulomb = 1.1 > > epsilon_r= 15 ; 2.5 (with polarizable water) > > vdw_type = cutoff ;cutoff (for use with Verlet-pairlist) > > > > rvdw_switch = 0.9 > > rvdw = 1.1 ;1.1 (for use with Verlet-pairlist) > > > > cutoff-scheme= verlet > > > > tcoupl = v-rescale > > tc-grps = LIPIDS SOL > > tau_t = 1.0 1.0 > > ref_t = 298 298 > > Pcoupl = parrinello-rahman > > Pcoupltype= semiisotropic > > tau_p = 12.0 > > compressibility = 3e-4 3e-4 ; 3e-4 > > ref_p = 1.0 1.0 ; 1.0 1.0 > > > > gen_vel= yes > > gen_temp = 298 > > gen_seed = 473529 > > > > constraints= none > > constraint_algorithm = Lincs > > continuation = no > > lincs_order= 4 > > lincs_warnangle= 30 > > > > Is there something that I can change in my mdp file? Or is there > something > > wrong with the lipid itself? > > > > > > Thank you > > Namit > > > > > -- > *Namit Chaudhary* > Chemical Engineering | Carnegie Mellon University > M: 724-506-0693 | E: nchau...@andrew.cmu.edu > -- > 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] Gromacs 2019 - Ryzen Architecture
Hi, A few things besides any Ryzen-specific issues. First, your pinoffset for the second one should be 16, not 17. The way yours is set up, you're running on cores 0-15, then Gromacs will detect that your second simulation parameters are invalid (because from cores 17-32, core 32 does not exist) and turn off core pinning. You can verify that in the log file. Second, 16 threads per simulation is overkill, and you can get gains from stealing from GPU down-time by running 2 simulations per GPU. So I would suggest something like mdrun -nt 8 -pin on -pinoffset 0 -gpu_id 0 & mdrun -nt 8 -pin on -pinoffset 8 -gpu_id 0 & mdrun -nt 8 -pin on -pinoffset 16 -gpu_id 1 & mdrun -nt 8 -pin on -pinoffset 24 -gpu_id 1 might give you close to optimal performance. On Thu, Jan 2, 2020 at 5:32 AM Paul bauer wrote: > Hello, > > we only added full detection and support for the newer Rizen chip-sets > with GROMACS 2019.5, so please try if the update to this version solves > your issue. > If not, please open an issue on redmine.gromacs.org so we can track the > problem and try to solve it. > > Cheers > > Paul > > On 02/01/2020 13:26, Sandro Wrzalek wrote: > > Hi, > > > > happy new year! > > > > Now to my problem: > > > > I use Gromacs 2019.3 and to try to run some simulations (roughly 30k > > atoms per system) on my PC which has the following configuration: > > > > CPU: Ryzen 3950X (overclocked to 4.1 GHz) > > > > GPU #1: Nvidia RTX 2080 Ti > > > > GPU #2: Nvidia RTX 2080 Ti > > > > RAM: 64 GB > > > > PSU: 1600 Watts > > > > > > Each run uses one GPU and 16 of 32 logical cores. Doing only one run > > at time (gmx mdrun -deffnm rna0 -gpu_id 0 -nb gpu -pme gpu) the GPU > > utilization is roughly around 84% but if I add a second run, the > > utilization of both GPUs drops to roughly 20%, while leaving logical > > cores 17-32 idle (I changed parameter gpu_id, accordingly). > > > > Adding additional parameters for each run: > > > > gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 0 -gpu_id 0 -nb gpu > > -pme gpu > > > > gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 17 -gpu_id 1 -nb gpu > > -pme gpu > > > > I get a utilization of 78% per GPU, which is nice but not near the 84% > > I got with only one run. In theory, however, it should come at least > > close to that utilization. > > > > I suspect, the Ryzen Chiplet design as the culprit since Gromacs seems > > to prefer the the first Chiplet, even if two simultaneous simulations > > have the resources to occupy both. The reason for the 78% utilization > > could be because of overhead between the two Chiplets via the infinity > > band. However, I have no proof, nor am I able to explain why gmx mdrun > > -deffnm rna0 -nt 16 -gpu_id 0 & 1 -nb gpu -pme gpu works as well - > > seems to occupy free logical cores then. > > > > Long story short: > > > > Are there any workarounds to squeeze the last bit out of my setup? Is > > it possible to choose the logical cores manually (I did not found > > anything in the docs so far)? > > > > > > Thank you for your help! > > > > > > Best, > > > > Sandro > > > > -- > Paul Bauer, PhD > GROMACS Development Manager > KTH Stockholm, SciLifeLab > 0046737308594 > > -- > 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] GROMOS forcefields
Thank you for such a detailed response. The explanation was very helpful. On Sat, Jan 4, 2020 at 10:00 PM Kenny Goossens wrote: > Hi Shakkira, > > In each of the consecutice iterations of the GROMOS force field, a > reparameterization of the constants was performed in order to reproduce > experimental data for various molecules (in the case of the GROMOS suite, > parameterization is mainly fitted to free enthalpy of solvation). For > GROMOS54a7, the focus was on improving behaviour of amino acids. Older > iterations of the force field have less parameters, and are in general less > accurate. This depends on the system you are working with, however. The > first number (43,56,...) stands for the number of atom types in the force > field, the last number stands for the iteration of the force field. Also > not that A and B versions are designed for different types of applications. > > I would advise you to look into the literature on the parameterization of > the force fields to get an idea of the improvements/changes in every > iteration of the force field. Furthermore, beware as the GROMOS force field > does not always show the intended behavior in newer versions of Gromacs, > and extra caution has to be taken in deciding on the simulation conditions. > The issues are illustrated i.e. in Reißer 2017m JCTC > (10.1021/acs.jctc.7b00178) And Silva et al 2018 JCTC > (10.1021/acs.jctc.8b00758). As far as I'm aware, the Gromacs team has > decided to discontinue support for GROMOS in the future for this reason. > > 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 shakira shukoor > > Verzonden: zaterdag 4 januari 2020 16:23 > Aan: gromacs.org_gmx-users@maillist.sys.kth.se < > gromacs.org_gmx-users@maillist.sys.kth.se> > Onderwerp: [gmx-users] GROMOS forcefields > > Hi all > Can anyone explain the different code seen in forcefields of GROMOS like > 53A6, 54A7, 43a1,. what does these numbers mean? > > -- > *Best Regards* > > Shakkira E > PhD student INSPIRE Scholar > Department of Chemistry > sdmdlab.xyz > IIT Patna > Bihta > Patna 801106 > -- > 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. > -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] [gmx-user] Autodock Vina Out use in gromacs MD
Dear Proffesor Lemkul, I have given below the MD RMSD for complex, and noted that Ligand is getting detached again. When I viewed the trajectory on VMD it was confirmed. The ligand did not abruptly got dislodged instead it slowly came out of binding pocket and started moving around after. https://drive.google.com/file/d/1IBMU-8SzSgXVr_h9zyeVwNV7kQ4at8-S/view?usp=sharing I know that following CGenFF tutorial and fixing the molecule and reparameterization would be the correct thing to do however I lack time at this moment. I read the paper and went through the tutorial and it's some what of a complex method to fix the parameters. I was thinking if I should use a different force-field such as Gromos with parameterization with ATB server. I have already submitted the given molecule below for optimization in ATB and the parameterization is now complete. Other option is to use Amber force field. Kindly let me know what your opinion on this. Molecule https://drive.google.com/file/d/1Ni8rUX4sH3aKaRhhXqCZr9w8VJVetCI7/view?usp=sharing Interactions at binding site us DS Visualizer https://drive.google.com/file/d/16EkWYDPDyTfkERiQgaOYo4XxYxqslOD0/view?usp=sharing Also please let me know if you think the given interactions are enough to keep the molecule at binding site for like 100ns? Thank you in Advance! Kind Regards Q On Tue, Dec 31, 2019 at 9:21 AM Justin Lemkul wrote: > > > On 12/30/19 1:51 PM, Quin K wrote: > > Further to following email, is it OK to do an energy minimization with > > Gaussian16 so the molecule is refined before MD simulation with Gromacs? > > What would be the purpose? A gas-phase optimized geometry has no > relationship to the pose adopted by a molecule upon binding to its > receptor. > > > If such an energy minimization is done should I use DFT ? > > Depends on the force field you're using. Most biomolecular force fields > do not use DFT for most calculations. If this goes back to our original > discussion about your CGenFF parameters, I beg you to follow the advice > I already gave - read the CGenFF paper. It tells you the *exact* model > chemistries you should use for everything to ensure compatibility with > the CHARMM force field. > > > Would that affect the orientation at which molecule was docked with > > protein? > > No, because the docking software changes the configuration. > > -Justin > > > > > On Mon, Dec 30, 2019 at 8:35 PM Quin K wrote: > > > >> Hi > >> > >> I noted when I used Autodock vina for docking and used the converted > back > >> .mol2 file from .pdbqt format, there were a lot of changes in the > molecule > >> than the molecule I initially submitted to Vina for docking. Like the > *atomic > >> charges were different. * > >> Is this normal? or is there a way to use the original DFT optimized > >> molecule with current docking orientation of Vina output file?? > >> Also noted that there were missing atoms like hydrogens. > >> Last time I tried this simulation the ligand got detached from binding > >> site after like 20 ns. This could probably be a main reason for that > >> because I never refined the molecule to adjust for changed charges etc. > >> > >> Kindly give your opinion > >> Thanks! > >> Regards! > >> > > -- > == > > 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.
Re: [gmx-users] GROMACS 2020 official release
Hello again, I got notified that there is an issue for the first link, it needs to be without the final dot: http://manual.gromacs.org/2020/release-notes/index.html Sorry for the inconvenience and happy new year! Cheers Paul On 01/01/2020 18:11, Paul bauer wrote: Hello GROMACS users! The official release of GROMACS 2020 is now available. What new things can you expect? Please see the release notes highlights at http://manual.gromacs.org/2020/release-notes/index.html. You can find the code, manual, release notes, installation instructions and test suite at the links below. Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.tar.gz Documentation: http://manual.gromacs.org/2020/index.html (includes install guide, user guide, reference manual, and release notes) Test Suite: http://gerrit.gromacs.org/download/regressiontests-2020.tar.gz Happy simulating! -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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] query regarding center of mass removal
On 1/4/20 1:38 AM, Snehasis Chatterjee wrote: Thank you Prof. Lemkul for your kind reply. In mdp file, I will set comm_grps to "system". But in tc-grps, can I couple capsid with Ca2+ ions? 240 Ca2+ ions are non-covalently attached with the capsid and have important role in maintaining capsid stability. I am also planing to run another set of simulation, where RNA is non-covalently attached with the capsid. In tc-grps, I can couple capsid, RNA and Ca2+ ions together. I am looking forward for your reply. Generally solute and solvent are coupled separately, however you define what the solute is. -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.
Re: [gmx-users] GROMOS forcefields
Very informative and interesting. I was using 54a7 forcefield with GROMACS 2018.4. I was confused with mdp parameters. Which version of GROMACS should I use if I want to employ 54a7 force field? On Sat, 4 Jan 2020, 22:00 Kenny Goossens, wrote: > Hi Shakkira, > > In each of the consecutice iterations of the GROMOS force field, a > reparameterization of the constants was performed in order to reproduce > experimental data for various molecules (in the case of the GROMOS suite, > parameterization is mainly fitted to free enthalpy of solvation). For > GROMOS54a7, the focus was on improving behaviour of amino acids. Older > iterations of the force field have less parameters, and are in general less > accurate. This depends on the system you are working with, however. The > first number (43,56,...) stands for the number of atom types in the force > field, the last number stands for the iteration of the force field. Also > not that A and B versions are designed for different types of applications. > > I would advise you to look into the literature on the parameterization of > the force fields to get an idea of the improvements/changes in every > iteration of the force field. Furthermore, beware as the GROMOS force field > does not always show the intended behavior in newer versions of Gromacs, > and extra caution has to be taken in deciding on the simulation conditions. > The issues are illustrated i.e. in Reißer 2017m JCTC > (10.1021/acs.jctc.7b00178) And Silva et al 2018 JCTC > (10.1021/acs.jctc.8b00758). As far as I'm aware, the Gromacs team has > decided to discontinue support for GROMOS in the future for this reason. > > 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 shakira shukoor > > Verzonden: zaterdag 4 januari 2020 16:23 > Aan: gromacs.org_gmx-users@maillist.sys.kth.se < > gromacs.org_gmx-users@maillist.sys.kth.se> > Onderwerp: [gmx-users] GROMOS forcefields > > Hi all > Can anyone explain the different code seen in forcefields of GROMOS like > 53A6, 54A7, 43a1,. what does these numbers mean? > > -- > *Best Regards* > > Shakkira E > PhD student INSPIRE Scholar > Department of Chemistry > sdmdlab.xyz > IIT Patna > Bihta > Patna 801106 > -- > 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] GROMOS forcefields
On 1/4/20 11:29 AM, Kenny Goossens wrote: Hi Shakkira, In each of the consecutice iterations of the GROMOS force field, a reparameterization of the constants was performed in order to reproduce experimental data for various molecules (in the case of the GROMOS suite, parameterization is mainly fitted to free enthalpy of solvation). For GROMOS54a7, the focus was on improving behaviour of amino acids. Older iterations of the force field have less parameters, and are in general less accurate. This depends on the system you are working with, however. The first number (43,56,...) stands for the number of atom types in the force field, the last number stands for the iteration of the force field. Also not that A and B versions are designed for different types of applications. I would advise you to look into the literature on the parameterization of the force fields to get an idea of the improvements/changes in every iteration of the force field. Furthermore, beware as the GROMOS force field does not always show the intended behavior in newer versions of Gromacs, and extra caution has to be taken in deciding on the simulation conditions. The issues are illustrated i.e. in Reißer 2017m JCTC (10.1021/acs.jctc.7b00178) And Silva et al 2018 JCTC (10.1021/acs.jctc.8b00758). As far as I'm aware, the Gromacs team has decided to discontinue support for GROMOS in the future for this reason. Another 2018 paper accused GROMACS of being buggy: https://pubs.acs.org/doi/10.1021/acs.jctc.8b00425 - that study has motivated the response from the core GROMACS developers (https://chemrxiv.org/articles/On_The_Importance_of_Accurate_Algorithms_for_Reliable_Molecular_Dynamics_Simulations/11474583/1) illustrating defects in the physical model used to derive many of the the GROMOS parameter sets; it's not a bug in GROMACS that is likely the issue. -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.
Re: [gmx-users] GROMOS forcefields
Hi Shakkira, In each of the consecutice iterations of the GROMOS force field, a reparameterization of the constants was performed in order to reproduce experimental data for various molecules (in the case of the GROMOS suite, parameterization is mainly fitted to free enthalpy of solvation). For GROMOS54a7, the focus was on improving behaviour of amino acids. Older iterations of the force field have less parameters, and are in general less accurate. This depends on the system you are working with, however. The first number (43,56,...) stands for the number of atom types in the force field, the last number stands for the iteration of the force field. Also not that A and B versions are designed for different types of applications. I would advise you to look into the literature on the parameterization of the force fields to get an idea of the improvements/changes in every iteration of the force field. Furthermore, beware as the GROMOS force field does not always show the intended behavior in newer versions of Gromacs, and extra caution has to be taken in deciding on the simulation conditions. The issues are illustrated i.e. in Reißer 2017m JCTC (10.1021/acs.jctc.7b00178) And Silva et al 2018 JCTC (10.1021/acs.jctc.8b00758). As far as I'm aware, the Gromacs team has decided to discontinue support for GROMOS in the future for this reason. 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 namens shakira shukoor Verzonden: zaterdag 4 januari 2020 16:23 Aan: gromacs.org_gmx-users@maillist.sys.kth.se Onderwerp: [gmx-users] GROMOS forcefields Hi all Can anyone explain the different code seen in forcefields of GROMOS like 53A6, 54A7, 43a1,. what does these numbers mean? -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- 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] GROMOS forcefields
Hi all Can anyone explain the different code seen in forcefields of GROMOS like 53A6, 54A7, 43a1,. what does these numbers mean? -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- 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] The pull code
Dear gromacs users, I am tryingto make a shear flow in an electrolyte by moving two parallel bilayers immersedin the electrolyte in opposite directions. I use the following pull code (wherethe groups low and up are the two moving bilayers): pull = yespull-coord1-type = umbrellapull-coord1-geometry= direction-periodicpull-pbc-ref-prev-step-com= yespull-coord1-dim = Y N Npull-coord1-vec = 1 0 0pull-coord1-start = yespull-ngroups = 2pull-group1-name = lowpull-group1-pbcatom= 2pull-group2-name = uppull-group2-pbcatom= 1202pull-coord1-groups= 1 2pull-coord1-rate = 0.030 pull-coord1-k = 500 pull-coord1-init = 1.3pull-nstxout = 250pull-nstfout = 250 I expect thevelocity of the bilayers to be ±15 m/s. But the calculated velocityprofile shows a velocity of around 5 m/s. I also tried some other rates ofchange of the reference position and found that the calculated velocity isalways around 3 times less than what I expect. Could you please let me know whatis the problem with my code? “It shouldbe noted that I am using Gromacs 2019 and that I didn’t encounter such problemwhen using the same code (minus the pull-pbc-ref-prev-step-comcommand) and the same simulation system in Gromacs 2016” Best wishes,Majid -- 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.
