[gmx-users] Energy analysis
Hi gromacs users, I want to calculate the energy for comparative analysis of protein with and without metal ion, wherein I would like to determine the influence of metal on protein structural stability. I have used gromacs for simulation. Please suggest me how to do this kind of analysis? Should i follow a specific tutorial? Amir -- 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] Turning off electrostatics between protein and water, then protein and protein
Hello, I am running simulations of two protein domains in tip4p water and 0.15M salt concentration that contain up to 650,000 atoms total. The protein domains are separated from each other at the start of each simulation and I am measuring how the distance between them changes over time. Now, I need to do the same simulations, but with electrostatics between proteins and water turned off (with water-water, protein-protein, ion-water, ion-protein electrostatics remaining). Then I need to repeat that, but additionally turning off electrostatics between the two domains. Water-water, ion-water, ion-protein, intra-domain electrostatics should remain on. What will be the best way to do this? I am using CHARMM27 force field and the following settings to run the production simulations: integrator = md dt = 0.002 nsteps = 100 ; 2ns nstlog = 1000 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstcalcenergy = 100 nstenergy = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 1.0 1.0 ref_t = 300.0 300.0 ; pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 5.0 compressibility = 4.5e-5 ref_p = 1.0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; nstcomm = 100 comm_mode = linear comm_grps = Protein Non-Protein ; refcoord_scaling= com I have tried to use the energy groups (energygrp-table) to specify interaction tables between water and protein, where I would set the electrostatic potential to zero. However, given that energygrp-table and Varlet cutoff-scheme are incompatible, I could not make it work. But it is possible that I did something wrong. Thank you in advance, Aram -- 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] Determining the cut offs more than half of the box
Hi, I don't understand what you think you want long cutoffs for. They are baked into the force field and you should not change those without reason to believe it already works. Mark On Sat, 18 Nov 2017 18:08 Iman Ahmadabadi wrote: > Dear Gromacs Users, > > I need to determine the 2.0 nm for VDW and Coulombic cut offs for my box > that its height along z direction is too small (for example 2.0 nm) but > the error will arise for me and I couldn't use the cut off more than 1.0 nm > because of the box size. What should I do in this regard? > > Best, > -- > 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] virtual site, dummy massive site
Hi, Yes those will affect what configurations are sampled, but not the LJ component of the energy of the configurations. Mark On Sat, 18 Nov 2017 23:54 Alex wrote: > And the things that affect the motion of the things with LJ interactions. > :) > > Alex > > > On 11/18/2017 3:49 PM, Mark Abraham wrote: > > Hi, > > > > Only things with LJ interactions can influence the LJ energy. > > > > Mark > > > > On Fri, 17 Nov 2017 21:06 Faezeh Pousaneh wrote: > > > >> I have 2 questions please. They seem evident, but I need to be sure to > >> solve my simulation problem: > >> > >> 1- Does being a virtual site (charge, no mass) or a normal atom, > effects on > >> its LJ interaction energies with rest of system? > >> > >> 2- Does adding a dummy massive site (no charge, only mass) to atoms of > >> mono-atomic system, influences on the LJ energy of whole system? > >> > >> Best regards > >> -- > >> 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] Restarting crashed simulation
Hi, Looks like you made a typo with state.cpt and that you perhaps have multiple mdrun processes running such that the actual output file is in one of the backup files labelled with # characters. Mark On Fri, 17 Nov 2017 19:37 Ali Ahmed wrote: > Hello GROMACS users > My MD simulation was crashed then I restarted the simulation from the point > when the point was written using this command on 64 processors: mpirun -np > 64 mdrun_mpi -s md.tpr -cpi stat.cpt > > After few days I got nothing in the folder usch as output.gro and I got the > following > ___ > Command line: > mdrun_mpi -s md.tpr -cpi stat.cpt > > Warning: No checkpoint file found with -cpi option. Assuming this is a new > run. > > > Back Off! I just backed up md.log to ./#md.log.2# > > Running on 4 nodes with total 64 cores, 64 logical cores > Cores per node: 16 > Logical cores per node: 16 > Hardware detected on host compute-2-27.local (the node of MPI rank 0): > CPU info: > Vendor: Intel > Brand: Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz > SIMD instructions most likely to fit this hardware: AVX_256 > SIMD instructions selected at GROMACS compile time: AVX_256 > > Hardware topology: Basic > > Reading file md.tpr, VERSION 2016.3 (single precision) > Changing nstlist from 10 to 40, rlist from 1 to 1.003 > > Will use 48 particle-particle and 16 PME only ranks > This is a guess, check the performance at the end of the log file > Using 64 MPI processes > Using 1 OpenMP thread per MPI process > > Non-default thread affinity set probably by the OpenMP library, > disabling internal thread affinity > WARNING: This run will generate roughly 50657 Mb of data > > starting mdrun 'Molecular Dynamics' > 2500 steps, 5.0 ps. > > step 888000 Turning on dynamic load balancing, because the performance loss > due to load imbalance is 8.7 %. > step 930400 Turning off dynamic load balancing, because it is degrading > performance. > step 1328000 Turning on dynamic load balancing, because the performance > loss due to load imbalance is 3.4 %. > step 1328800 Turning off dynamic load balancing, because it is degrading > performance. > step 1336000 Turning on dynamic load balancing, because the performance > loss due to load imbalance is 3.4 %. > step 1338400 Turning off dynamic load balancing, because it is degrading > performance. > step 134 Will no longer try dynamic load balancing, as it degraded > performance. > Writing final coordinates. > Average load imbalance: 13.2 % > Part of the total run time spent waiting due to load imbalance: 7.5 % > Average PME mesh/force load: 1.077 > Part of the total run time spent waiting due to PP/PME imbalance: 4.1 % > > NOTE: 7.5 % of the available CPU time was lost due to load imbalance > in the domain decomposition. > You might want to use dynamic load balancing (option -dlb.) > > >Core t (s) Wall t (s)(%) >Time: 26331875.601 411435.556 6400.0 > 4d18h17:15 > (ns/day)(hour/ns) > Performance: 10.5002.286 > _ > > Any advise or suggestion will be helpful. > > Thanks in advance > -- > 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] virtual site, dummy massive site
And the things that affect the motion of the things with LJ interactions. :) Alex On 11/18/2017 3:49 PM, Mark Abraham wrote: Hi, Only things with LJ interactions can influence the LJ energy. Mark On Fri, 17 Nov 2017 21:06 Faezeh Pousaneh wrote: I have 2 questions please. They seem evident, but I need to be sure to solve my simulation problem: 1- Does being a virtual site (charge, no mass) or a normal atom, effects on its LJ interaction energies with rest of system? 2- Does adding a dummy massive site (no charge, only mass) to atoms of mono-atomic system, influences on the LJ energy of whole system? Best regards -- 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] (no subject)
Hi, Yes, modulo any exclusions you used. Mark On Fri, 17 Nov 2017 18:50 Faezeh Pousaneh wrote: > Hi, > > I have a simple system of non-charged diatomic molecule, (A-B). > > I expect total LJ interaction energy in such system when we put LJ > parameters of atom B zero (c6 and c12=0) should be equal with total LJ > energy of a system containing only atom A. > Am I right? > > Best regards > -- > 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] virtual site, dummy massive site
Hi, Only things with LJ interactions can influence the LJ energy. Mark On Fri, 17 Nov 2017 21:06 Faezeh Pousaneh wrote: > I have 2 questions please. They seem evident, but I need to be sure to > solve my simulation problem: > > 1- Does being a virtual site (charge, no mass) or a normal atom, effects on > its LJ interaction energies with rest of system? > > 2- Does adding a dummy massive site (no charge, only mass) to atoms of > mono-atomic system, influences on the LJ energy of whole system? > > Best regards > -- > 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] Determining the cut offs more than half of the box
Dear Gromacs Users, I need to determine the 2.0 nm for VDW and Coulombic cut offs for my box that its height along z direction is too small (for example 2.0 nm) but the error will arise for me and I couldn't use the cut off more than 1.0 nm because of the box size. What should I do in this regard? Best, -- 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] c_6 and c_12 to zero
Hi, I have a simple system of non-charged diatomic molecule, (A-B). I expect total LJ interaction energy in such system when we put LJ parameters of atom B zero (c6 and c12=0) should be equal with total LJ energy of a system containing only atom A. Am I right? Best regards -- 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] virtual site, dummy massive site LJ interactions
Hi, I have 2 questions please. They seem evident, but I need to be sure to solve my simulation problem: 1- Does being a virtual site (charge, no mass) or a normal atom, effects on its LJ interaction energies with rest of system? 2- Does adding a dummy massive site (no charge, only mass) to atoms of mono-atomic system, influences on the LJ energy of whole system? Best regards -- 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.
