Re: [gmx-users] Coulomb term calculation in gromacs
On 11/22/19 11:08 AM, nikol...@spbau.ru wrote: Dear all, I have a question about the calculation of the Coulomb term in Gromacs. As I understand, two terms are involved: Coulomb 1-4, which is calculated among the 1st and 4th atoms, and the term for the rest of the interactions. In the manual the standard Coulomb formula is given with f = 138.935..., is it applied for the Coulomb 1-4 interactions? Electrostatics are calculated the same way everywhere (within the short-range cutoff), unless the force field applies a scaling factor to this interaction (fudgeQQ). If I use the electrostatic scheme Cut-off, then the usual Coulomb formula is applied for all atoms within the cutoff, excluding the 1-2, 1-3 and 1-4 bonded atoms? Yes. If I use the PME scheme, then interactions between all atoms within the rlist is calculated, excluding the 1-2, 1-3 and 1-4 bonded atoms, by applying the Ewald sum? Interactions within rlist (direct space) are computed by the normal (shifted) Coulomb potential. Also, I have generated a model system of H2 molecule for gromacs and put charges on both atoms, calculated the energy terms. However, the Coulomb 1-4 was not zero. How could that be? Was that related to the PBC & PME is used? A diatomic molecule cannot have 1-4 interactions, unless you have added [pairs] for the 1-2 interaction, which mdrun will interpret as a 1-4 interaction (because in that case, it's what you've told it to do). A pair interaction would be incorrect for a diatomic molecule. -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] anisotropic polarization
On 11/22/19 3:53 AM, Amin Rouy wrote: Hi, Is anisotropic polarization implemented in Gromacs. I find a paper by Justin; ''Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model'' How can I apply it to my own molecules? By careful parametrization of the anisotropic polarization tensor :) The implementation in our Drude model is not yet in the official documentation (nor is the code, though I'm making headway there). You can pull the "drude" branch from the git repo and look at the implementation and syntax. Be advised that this isn't just something you can add to molecules without really precise parametrization. -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.
[gmx-users] Clarification on gpu acceleration for rf type dataset
Hi, Gromacs documentation states the following"Native GPU acceleration issupported with the Verlet cut-offscheme (not with the group scheme) with PME, reaction-field, andplain cut-off electrostatics." In source code tracing, there’s no further GPUkernel launched for rf type dataset except PP (non-bonded short-range).I would like to confirm that gpu acceleration for rf type dataset is limited to PP task. -vicky -- 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] anisotropic polarization
Den 2019-11-22 kl. 09:53, skrev Amin Rouy: Hi, Is anisotropic polarization implemented in Gromacs. I find a paper by Justin; ''Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model'' How can I apply it to my own molecules? Thank you for help. There is just one (rather obscure) anisotropically polarizable water model implemented. There is a topology called sw.itp, but there are better (isotropic) models out there. https://pubs.acs.org/doi/10.1021/jp003843l -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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] gmx rdf selrpos seltype
Dear gmx users, I am calculating a spherical radial distribution function between the center of mass of the methyl group of STS (my surfactant) around the center of mass of the STS micelle. I am using this command: gmx rdf -f production_NpT.xtc -n index.ndx -s production_NpT.tpr -selrpos whole_mol_com -seltype atom -b 8 -ref ST -sel C2 -o output.xvg and I get my graph. If I switch selrpose with seltype and I type: gmx rdf -f production_NpT.xtc -n index.ndx -s production_NpT.tpr -seltype whole_mol_com -selrpose atom -b 8 -ref C2 -sel ST -o output.xvg I get a different result. If I well understood, in the first case the reference position is the center of mass the micelle and in the second case the reference position is the methyl group. Teorically I should get the same result, maybe there is something in selrpos and seltype which I missed. Can anyone help me? Thanks a lot Giuseppe -- 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] Coulomb term calculation in gromacs
Dear all, I have a question about the calculation of the Coulomb term in Gromacs. As I understand, two terms are involved: Coulomb 1-4, which is calculated among the 1st and 4th atoms, and the term for the rest of the interactions. In the manual the standard Coulomb formula is given with f = 138.935..., is it applied for the Coulomb 1-4 interactions? If I use the electrostatic scheme Cut-off, then the usual Coulomb formula is applied for all atoms within the cutoff, excluding the 1-2, 1-3 and 1-4 bonded atoms? If I use the PME scheme, then interactions between all atoms within the rlist is calculated, excluding the 1-2, 1-3 and 1-4 bonded atoms, by applying the Ewald sum? Also, I have generated a model system of H2 molecule for gromacs and put charges on both atoms, calculated the energy terms. However, the Coulomb 1-4 was not zero. How could that be? Was that related to the PBC & PME is used? Best regards, Dmitrii -- 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] Superparamagnetism
Hi everyone, Is it possible to simulate* superparamagnetism* in Gromacs? thanks for answer. -- 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] How to properly use tune_pme?
Hi, > Am 21.11.2019 um 17:15 schrieb Marcin Mielniczuk : > > Hi, > > I'm trying to make use of tune_pme to find out the optimal number of PME > ranks. My command line is: > UCX_LOG_LEVEL=info MPIRUN="mpirun" ./gmx_mpi tune_pme -v -s > ../tip4p_min2 -mdrun "./gmx_mpi mdrun" -np 4 > When started in such a way, Gromacs exits with a fatal error, as shown > in the attached log file, `tune_pme.txt`. OTOH, benchtest.log is empty. > While these logs were created using Gromacs 2019.3, the same issue > persists with 2019.4. > > Manually executing the command `mpirun -np 4 ./gmx_mpi mdrun -version > -maxh 0.001` succeeds, as in the attached log file `mpirun.txt`. > > What's the correct way to use tune_pme then? Try compiling tune_pme without MPI, but then call the MPI-enabled mdrun: gmx tune_pme -s ../tip4p_min2 -mdrun "./gmx_mpi mdrun" -np 4 Regards, Carsten > It looks to me that what I'm doing is exactly what the documentation > says to. > > Thanks, > Marcin > -- > 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] number and size of NaCl crystals formed
Dear users, I have a question. I simulated Membrane Crystallization process with NaCl salt, using different types of polymeric membranes models. At this moment I'm able to evaluate the order that bring to nucleation and sequently crystallization, but I'm not able to evaluate number and size of NaCl crystals formed after several times for the different models. I found in Gromacs Manual the command gmx clustsize, but I don't understand the meaning of this, and If I can apply it for my purpose. Can anyone to help me? Best regards Maria Luisa Maria Luisa Perrotta Ph.D Student, CNR-ITM via P.Bucci, 87036 Rende (Cs) Italy email: ml.perro...@itm.cnr.it -- 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] anisotropic polarization
Hi, Is anisotropic polarization implemented in Gromacs. I find a paper by Justin; ''Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model'' How can I apply it to my own molecules? Thank you for help. -- 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.
