Re: [gmx-users] Simulation for Metalloprotein
The standard force fields (charmm, amber, etc) all have calcium, as well as many other metals. Please actually try running pdb2gmx before asking the list if it will work. On Tue, Feb 27, 2018 at 5:12 AM, Sankaran SV . <119013...@sastra.ac.in> wrote: > Hi users, > > Whether it is possible to run the simulation for protein with metal > (calcium) ? > If so, what are the force fields that can be used ? > How those force fields must be altered in order to run the simulation. > > > -- > Sankaran.s.v > bbin > -- > 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. > -- Joe Jordan -- 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] Installing DSSP
Hi, I use gromacs version 5.1.4 through cygwin Please let me know how to install DSSP? Which version of DSSP would be compatible with the above version of gromacs? Thanks, Neha -- 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] Installing DSSP
Hi, Start with http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-do_dssp.html Mark On Tue, Feb 27, 2018 at 1:00 PM Neha Gupta wrote: > Hi, > > I use gromacs version 5.1.4 through cygwin > > Please let me know how to install DSSP? > > Which version of DSSP would be compatible with the above version of > gromacs? > > Thanks, > Neha > -- > 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] Equilibration
Hi, I run a simulation of a solute in water. I have 2 question please: 1- After NVT equilibrium, I see that all quantities like energies and temperature become stable, except pressure. Should I continue till pressure also goes stable? or can I move forward and do it in production run? 2- My interest production run is NVT, should I run 2th-step-equilibrium with NPT also? or only NVT equilibration is enough? -- 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] 2018 performance question
Hi, I did a number of test runs with gmx versions 2018 vs 2016.5, both on workstations with either GTX 780 or GTX1060 (CPU and other hardwareidentical: Intel Core i7-4930K CPU @ 3.40GHz, 6 cores, each two threads) the system is an amorphous sample of some small organic molecule (a glass,about 5500 atoms, 250 molecules) at ambient pressure, plus a bit of simulatedannealing, otherwise vanilla MD (mdp below) performance details in the table below. what i see, in a nutshell, is: 1 for this system and hardware 2018 is about 50% faster than 2016 (good) 2 GTX1060 is about 25% faster than GTX 780 (rather disappointing considering the $$$) 3 playing with different mdrun options (-nt, -pin, -pme, etc...) did in no case improve speed. compared to leaving all decisions to gromacs (smart gmx) 4 running of 2 jobs on the same node simultaneously, and splitting the cores, does not improve overall performance although the CPU appears to be under-used compared to the GPU in all cases in particular point 4 surprised me, and i wonder if anybody can suggest options i didn't trythat might result in a better performance!? (details from log files for individual cases canbe supplied if that helps) cheers,michael the table: first column: gmx version, second column: performance (ns/d). "x2" next to the versionmeans that two jobs were run simultaneously on a single node (in these cases the performance value isthe sum of the values from the two individual cases for a fair comparison) third column: the mdrun command with all options used in each case. GTX 1060 2016 171.1 gmx mdrun -v -deffnm mcz 2016x2 141.8 gmx mdrun -nt 6 -v -ntmpi 1 -ntomp 6 -pin on -pinoffset 0 -deffnm mcz1 gmx mdrun -nt 6 -v -ntmpi 1 -ntomp 6 -pin on -pinoffset 6 -deffnm mcz2 2016x2 119.5 gmx mdrun -v -nt 6 -pin on -pinoffset 0 -pinstride 1 -deffnm mcz1 gmx mdrun -v -nt 6 -pin on -pinoffset 3 -pinstride 1 -deffnm mcz2 2018 255.6 gmx mdrun -v -deffnm mcz 2018x2 245.6 gmx mdrun -v -deffnm mcz1 gmx mdrun -v -deffnm mcz2 2018x2 190.7 gmx mdrun -v -nt 6 -pin on -pinoffset 0 -pinstride 1 -deffnm mcz1 gmx mdrun -v -nt 6 -pin on -pinoffset 3 -pinstride 1 -deffnm mcz2 2018 223.9 gmx mdrun -v -deffnm mcz -pmefft cpu 2018 136.8 gmx mdrun -v -deffnm mcz -nt 12 -ntmpi 2 -ntomp 6 2018 138.1 gmx mdrun -v -deffnm mcz -nt 12 -ntmpi 2 -ntomp 6 -pmefft cpu 2018x2 168.0 gmx mdrun -v -deffnm mcz1 -nt 6 -ntmpi 1 -ntomp 6 -pin on -pinoffset 0 -pinstride 1 -pmefft cpu gmx mdrun -v -deffnm mcz2 -nt 6 -ntmpi 1 -ntomp 6 -pin on -pinoffset 3 -pinstride 1 -pmefft cpu 2018 222.0 gmx mdrun -nt 12 -v -deffnm mcz -pme cpu GTX 780 === 2016 188.0 gmx mdrun -v -deffnm mcz 2016x2 155.3 gmx mdrun -nt 6 -v -ntmpi 1 -ntomp 6 -pin on -pinoffset 0 -deffnm mcz1 gmx mdrun -nt 6 -v -ntmpi 1 -ntomp 6 -pin on -pinoffset 6 -deffnm mcz2 2016x2 112.7 gmx mdrun -v -nt 6 -pin on -pinoffset 0 -pinstride 1 -deffnm mcz1 gmx mdrun -v -nt 6 -pin on -pinoffset 3 -pinstride 1 -deffnm mcz2 2018 202.8 gmx mdrun -v -deffnm mcz 2018x2 198.3 gmx mdrun -v -deffnm mcz1 gmx mdrun -v -deffnm mcz2 2018x2 DEAD gmx mdrun -v -nt 6 -pin on -pinoffset 0 -pinstride 1 -deffnm mcz1 gmx mdrun -v -nt 6 -pin on -pinoffset 3 -pinstride 1 -deffnm mcz2 the above jobs died on me without further notice, both gmx processes were still running (used CPU as seen with top) but gave no more output 2018 203.5 gmx mdrun -v -deffnm mcz -pmefft cpu 2018 136.9 gmx mdrun -v -deffnm mcz -nt 12 -ntmpi 2 -ntomp 6 2018 137.1 gmx mdrun -v -deffnm mcz -nt 12 -ntmpi 2 -ntomp 6 -pmefft cpu 2018x2 152.8 gmx mdrun -v -deffnm mcz1 -nt 6 -ntmpi 1 -ntomp 6 -pin on -pinoffset 0 -pinstride 1 -pmefft cpu gmx mdrun -v -deffnm mcz2 -nt 6 -ntmpi 1 -ntomp 6 -pin on -pinoffset 3 -pinstride 1 -pmefft cpu 2018 188.4 gmx mdrun -nt 12 -v -deffnm mcz -pme cpu mdp-file integrator = md dt = 0.001 nsteps = 100 comm-grps = System ; nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy = 1000 ; nstlist = 40 ns_type = grid pbc = xyz rlist = 1.2 cutoff-scheme = Verlet ; coulombtype = PME rcoulomb = 1.2 vdw_type = cut-off rvdw = 1.2 ; constraints = none ; tcoupl = v-rescale tau-t = 0.1 ref-t = 300 tc-grps = System ; pcoupl = berendsen pcoupltype = anisotropic tau-p = 2.0 compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref-p = 1 1 1 0 0 0 ; annealing = single annealing-npoints = 2 annealing-time = 0 10 annealing-temp = 511 491 From: Szilárd Páll To: Michael Bruns
[gmx-users] Question about gmx bar
Hi everyone, I just finished running 2 sets of simulations (ligand in water and RNA+ligand in water) for my system to learn about its binding energy. Using the parameter for BAR method, I ran 20 simulations for ligand in water and 30 simulations for RNA+ligand in water with different lambda stages. What is interesting/confusing to me is the 0 energy from stages 0-10. Based on what I have been reading and the set up of my prod.mdp, these stages should give Coulomb Energy. If you can tell me why or how to fix it, I would greatly appreciate your help. point 0 - 1, DG 0.00 +/- 0.00 point 1 - 2, DG 0.00 +/- 0.00 point 2 - 3, DG 0.00 +/- 0.00 point 3 - 4, DG 0.00 +/- 0.00 point 4 - 5, DG 0.00 +/- 0.00 point 5 - 6, DG 0.00 +/- 0.00 point 6 - 7, DG 0.00 +/- 0.00 point 7 - 8, DG 0.00 +/- 0.00 point 8 - 9, DG 0.00 +/- 0.00 point 9 - 10, DG 0.00 +/- 0.00 point 10 - 11, DG 1198.03 +/- 11.41 point 11 - 12, DG 711.32 +/- 1.58 point 12 - 13, DG 258.19 +/- 3.80 point 13 - 14, DG -116.21 +/- 3.81 point 14 - 15, DG 24.24 +/- 0.17 point 15 - 16, DG 25.40 +/- 0.18 point 16 - 17, DG 51.57 +/- 0.42 point 17 - 18, DG 51.20 +/- 0.57 point 18 - 19, DG 48.42 +/- 0.97 point 19 - 20, DG 46.55 +/- 0.56 point 20 - 21, DG 44.53 +/- 0.23 point 21 - 22, DG 20.56 +/- 0.12 point 22 - 23, DG 18.23 +/- 0.11 point 23 - 24, DG 13.64 +/- 0.16 point 24 - 25, DG -3.58 +/- 0.84 point 25 - 26, DG -44.60 +/- 0.29 point 26 - 27, DG -33.45 +/- 0.07 point 27 - 28, DG -15.22 +/- 0.02 point 28 - 29, DG 0.81 +/- 0.12 total 0 - 29, DG 2299.63 +/- 5.17 Here is the prod.mdp for complex: ; ; Production simulation ; ; ; RUN CONTROL ; integrator = sd; stochastic leap-frog integrator nsteps = 5000; 2 * 500,000 fs = 1000 ps = 1 ns dt = 0.002 ; 2 fs comm-mode= Linear; remove center of mass translation nstcomm = 100 ; frequency for center of mass motion removal ; ; OUTPUT CONTROL ; nstxout= 0 ; don't save coordinates to .trr nstvout= 0 ; don't save velocities to .trr nstfout= 0 ; don't save forces to .trr nstxout-compressed = 1000 ; xtc compressed trajectory output every 1000 steps (2 ps) compressed-x-precision = 1000 ; precision with which to write to the compressed trajectory file nstlog = 1000 ; update log file every 2 ps nstenergy = 1000 ; save energies every 2 ps nstcalcenergy = 100; calculate energies every 100 steps ; ; BONDS ; constraint_algorithm = lincs ; holonomic constraints constraints= all-bonds ; hydrogens only are constrained lincs_iter = 1 ; accuracy of LINCS (1 is default) lincs_order= 4 ; also related to accuracy (4 is default) lincs-warnangle= 30 ; maximum angle that a bond can rotate before LINCS will complain (30 is default) continuation = yes; formerly known as 'unconstrained-start' - useful for exact continuations and reruns ; ; NEIGHBOR SEARCHING ; cutoff-scheme = Verlet ns-type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs (default is 10) rlist = 1.0; short-range neighborlist cutoff (in nm) pbc = xyz; 3D PBC ; ; ELECTROSTATICS ; coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) ewald_geometry = 3d ; Ewald sum is performed in all three dimensions pme-order= 6; interpolation order for PME (default is 4) fourierspacing = 0.10 ; grid spacing for FFT ewald-rtol = 1e-6 ; relative strength of the Ewald-shifted direct potential at rcoulomb ; ; VDW ; vdw-type= PME rvdw= 1.0 vdw-modifier= Potent
[gmx-users] Output forces only for select group of atoms
Dear GROMACS users, I am simulating a fairly large system of about 25 atoms and I want to analyze the forces at each output step for only a select group of about 200 atoms (and actually only the z component of the force but this is less important). My question is whether or not there is a simple way to selectively output forces for only my atoms of interest. I will have long runs and high output frequency so I would really like to avoid having to output force data for the other ~249800 atoms in my system. Any help is greatly appreciated! Thanks, Jake Spooner -- 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] Output forces only for select group of atoms
Hi, No, but instead see http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html#re-running-a-simulation Mark On Tue, Feb 27, 2018 at 10:28 PM Jacob Alan Spooner wrote: > Dear GROMACS users, > > I am simulating a fairly large system of about 25 atoms and I want to > analyze the forces at each output step for only a select group of about 200 > atoms (and actually only the z component of the force but this is less > important). My question is whether or not there is a simple way to > selectively output forces for only my atoms of interest. I will have long > runs and high output frequency so I would really like to avoid having to > output force data for the other ~249800 atoms in my system. Any help is > greatly appreciated! > > Thanks, > Jake Spooner > -- > 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] Question about gmx bar
On 2/27/18 4:13 PM, Thanh Le wrote: Hi everyone, I just finished running 2 sets of simulations (ligand in water and RNA+ligand in water) for my system to learn about its binding energy. Using the parameter for BAR method, I ran 20 simulations for ligand in water and 30 simulations for RNA+ligand in water with different lambda stages. What is interesting/confusing to me is the 0 energy from stages 0-10. Based on what I have been reading and the set up of my prod.mdp, these stages should give Coulomb Energy. If you can tell me why or how to fix it, I would greatly appreciate your help. You've defined only a bonded transformation in those stages: bonded-lambdas = 0.0 0.01 0.025 0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 coul-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 Your electrostatic terms remain in state A (lambda = 0) and there is no difference in bonded energies, so the first windows are essentially doing nothing. -Justin point 0 - 1, DG 0.00 +/- 0.00 point 1 - 2, DG 0.00 +/- 0.00 point 2 - 3, DG 0.00 +/- 0.00 point 3 - 4, DG 0.00 +/- 0.00 point 4 - 5, DG 0.00 +/- 0.00 point 5 - 6, DG 0.00 +/- 0.00 point 6 - 7, DG 0.00 +/- 0.00 point 7 - 8, DG 0.00 +/- 0.00 point 8 - 9, DG 0.00 +/- 0.00 point 9 - 10, DG 0.00 +/- 0.00 point 10 - 11, DG 1198.03 +/- 11.41 point 11 - 12, DG 711.32 +/- 1.58 point 12 - 13, DG 258.19 +/- 3.80 point 13 - 14, DG -116.21 +/- 3.81 point 14 - 15, DG 24.24 +/- 0.17 point 15 - 16, DG 25.40 +/- 0.18 point 16 - 17, DG 51.57 +/- 0.42 point 17 - 18, DG 51.20 +/- 0.57 point 18 - 19, DG 48.42 +/- 0.97 point 19 - 20, DG 46.55 +/- 0.56 point 20 - 21, DG 44.53 +/- 0.23 point 21 - 22, DG 20.56 +/- 0.12 point 22 - 23, DG 18.23 +/- 0.11 point 23 - 24, DG 13.64 +/- 0.16 point 24 - 25, DG -3.58 +/- 0.84 point 25 - 26, DG -44.60 +/- 0.29 point 26 - 27, DG -33.45 +/- 0.07 point 27 - 28, DG -15.22 +/- 0.02 point 28 - 29, DG 0.81 +/- 0.12 total 0 - 29, DG 2299.63 +/- 5.17 Here is the prod.mdp for complex: ; ; Production simulation ; ; ; RUN CONTROL ; integrator = sd; stochastic leap-frog integrator nsteps = 5000; 2 * 500,000 fs = 1000 ps = 1 ns dt = 0.002 ; 2 fs comm-mode= Linear; remove center of mass translation nstcomm = 100 ; frequency for center of mass motion removal ; ; OUTPUT CONTROL ; nstxout= 0 ; don't save coordinates to .trr nstvout= 0 ; don't save velocities to .trr nstfout= 0 ; don't save forces to .trr nstxout-compressed = 1000 ; xtc compressed trajectory output every 1000 steps (2 ps) compressed-x-precision = 1000 ; precision with which to write to the compressed trajectory file nstlog = 1000 ; update log file every 2 ps nstenergy = 1000 ; save energies every 2 ps nstcalcenergy = 100; calculate energies every 100 steps ; ; BONDS ; constraint_algorithm = lincs ; holonomic constraints constraints= all-bonds ; hydrogens only are constrained lincs_iter = 1 ; accuracy of LINCS (1 is default) lincs_order= 4 ; also related to accuracy (4 is default) lincs-warnangle= 30 ; maximum angle that a bond can rotate before LINCS will complain (30 is default) continuation = yes; formerly known as 'unconstrained-start' - useful for exact continuations and reruns ; ; NEIGHBOR SEARCHING ; cutoff-scheme = Verlet ns-type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs (default is 10) rlist = 1.0; short-range neighborlist cutoff (in nm) pbc = xyz; 3D PBC ;
Re: [gmx-users] Equilibration
On 2/27/18 10:05 AM, Amin Rouy wrote: Hi, I run a simulation of a solute in water. I have 2 question please: 1- After NVT equilibrium, I see that all quantities like energies and temperature become stable, except pressure. Should I continue till pressure also goes stable? or can I move forward and do it in production run? Pressure isn't a conserved quantity in NVT. It is in NPT (hence the P). 2- My interest production run is NVT, should I run 2th-step-equilibrium with NPT also? or only NVT equilibration is enough? Model whatever conditions are relevant to you; even with NVT, you may want to simulate at a fixed density, which requires NPT equilibration to stabilize the pressure/density and then continue with NVT. Rarely is the initial configuration ideal. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Output forces only for select group of atoms
Hi Mark, Thank you for your speedy reply. Unfortunately I do not think a rerun will solve my problem since in that case I will just have to output coordinates of the entire system at my desired output frequency for the forces, and will still be generating huge trajectory files. Ideally I would be outputting the coordinates of the entire system very very infrequently (since I am not really interested in the coordinates), and outputting the forces for a small group of atoms very frequently. So in this case I don't think doing a rerun will save me anyting and will just add a post-processing step. Normally this would not be an issue but I will be running many simulations of these 25 atom systems at once, so outputting all the forces (or coordinates) when I only care about a fraction of them will be a significant problem. If anybody else has any ideas about how I could get around this issue I would be thankful, but I suspect there is no simple solution. Best, Jake From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: Tuesday, February 27, 2018 1:47 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Output forces only for select group of atoms Hi, No, but instead see http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html#re-running-a-simulation Mark On Tue, Feb 27, 2018 at 10:28 PM Jacob Alan Spooner wrote: > Dear GROMACS users, > > I am simulating a fairly large system of about 25 atoms and I want to > analyze the forces at each output step for only a select group of about 200 > atoms (and actually only the z component of the force but this is less > important). My question is whether or not there is a simple way to > selectively output forces for only my atoms of interest. I will have long > runs and high output frequency so I would really like to avoid having to > output force data for the other ~249800 atoms in my system. Any help is > greatly appreciated! > > Thanks, > Jake Spooner > -- > 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] Output forces only for select group of atoms
On 2/27/18 6:16 PM, Jacob Alan Spooner wrote: Hi Mark, Thank you for your speedy reply. Unfortunately I do not think a rerun will solve my problem since in that case I will just have to output coordinates of the entire system at my desired output frequency for the forces, and will still be generating huge trajectory files. Ideally I would be outputting the coordinates of the entire system very very infrequently (since I am not really interested in the coordinates), and outputting the forces for a small group of atoms very frequently. So in this case I don't think doing a rerun will save me anyting and will just add a post-processing step. Normally this would not be an issue but I will be running many simulations of these 25 atom systems at once, so outputting all the forces (or coordinates) when I only care about a fraction of them will be a significant problem. If anybody else has any ideas about how I could get around this issue I would be thankful, but I suspect there is no simple solution. Short of modifying the code, the only option is what Mark suggested. GROMACS isn't designed to do what you're asking. -Justin Best, Jake From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: Tuesday, February 27, 2018 1:47 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Output forces only for select group of atoms Hi, No, but instead see http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html#re-running-a-simulation Mark On Tue, Feb 27, 2018 at 10:28 PM Jacob Alan Spooner wrote: Dear GROMACS users, I am simulating a fairly large system of about 25 atoms and I want to analyze the forces at each output step for only a select group of about 200 atoms (and actually only the z component of the force but this is less important). My question is whether or not there is a simple way to selectively output forces for only my atoms of interest. I will have long runs and high output frequency so I would really like to avoid having to output force data for the other ~249800 atoms in my system. Any help is greatly appreciated! Thanks, Jake Spooner -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Equilibration
Not sure about with constant volume, as I don't tend to run under those conditions, but with constant pressure the pressure will always fluctuate quite substantially. How big the fluctuation is depends on the size of the system, the later the system is, the smaller the fluctuations. Small system (6k): https://twitter.com/dr_dbw/status/968624615063937025 Larger system (300k): https://twitter.com/dr_dbw/status/968625462959210496 You really should run a component with NPT, so that the system reaches the correct box size and pressure. It is unlikely that the box you set has the exact right dimensions and number of molecules to give the correct pressure/density. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On 28 February 2018 at 02:05, Amin Rouy wrote: > Hi, > > I run a simulation of a solute in water. I have 2 question please: > > 1- After NVT equilibrium, I see that all quantities like energies and > temperature become stable, except pressure. Should I continue till pressure > also goes stable? or can I move forward and do it in production run? > > 2- My interest production run is NVT, should I run 2th-step-equilibrium > with NPT also? or only NVT equilibration is enough? > -- > 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] Deleting a folder
Hello GROMACS users, I'm sorry for the crazy things I did. I was trying to update electric filed code for magnetic filed implementation by adding the cross product term to the force calculation equation. unfortunately, I failed and deleted the mdlib folder (GROMACS 5.1.2). The surprising thing is that GROMAS still applies electric filed. My question is, how does GROMACS apply electric field while the code is deleted? Best Ali -- 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] Deleting a folder
On 2/27/18 6:23 PM, Ali Ahmed wrote: Hello GROMACS users, I'm sorry for the crazy things I did. I was trying to update electric filed code for magnetic filed implementation by adding the cross product term to the force calculation equation. unfortunately, I failed and deleted the mdlib folder (GROMACS 5.1.2). The surprising thing is that GROMAS still applies electric filed. My question is, how does GROMACS apply electric field while the code is deleted? Deleting source code has no effect on software that's already installed. If you try to install again, then your compilation would fail due to missing files. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Question about gmx bar
Hi Justin, I assume, in order to get Coulomb energy for the first 10 stages, I should change coul-lambdas stages to the same row as bonded-lambdas (0.0 0.01 0.025 0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0). Is there another way to do it? Is there a paper I can read to get more details about the subject? Thanks, Thanh Le On 2/27/18 4:13 PM, Thanh Le wrote: > Hi everyone, > I just finished running 2 sets of simulations (ligand in water and RNA+ligand > in water) for my system to learn about its binding energy. Using the > parameter for BAR method, I ran 20 simulations for ligand in water and 30 > simulations for RNA+ligand in water with different lambda stages. What is > interesting/confusing to me is the 0 energy from stages 0-10. Based on what I > have been reading and the set up of my prod.mdp, these stages should give > Coulomb Energy. If you can tell me why or how to fix it, I would greatly > appreciate your help. You've defined only a bonded transformation in those stages: bonded-lambdas = 0.0 0.01 0.025 0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 coul-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 Your electrostatic terms remain in state A (lambda = 0) and there is no difference in bonded energies, so the first windows are essentially doing nothing. -Justin -- 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] Question about gmx bar
On 2/27/18 6:31 PM, Thanh Le wrote: Hi Justin, I assume, in order to get Coulomb energy for the first 10 stages, I should change coul-lambdas stages to the same row as bonded-lambdas (0.0 0.01 0.025 0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0). Is there another way to do it? Is there a paper I can read to get more details about the subject? No, but there's a tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html And other material on, e.g. alchemistry.org. -Justin Thanks, Thanh Le On 2/27/18 4:13 PM, Thanh Le wrote: Hi everyone, I just finished running 2 sets of simulations (ligand in water and RNA+ligand in water) for my system to learn about its binding energy. Using the parameter for BAR method, I ran 20 simulations for ligand in water and 30 simulations for RNA+ligand in water with different lambda stages. What is interesting/confusing to me is the 0 energy from stages 0-10. Based on what I have been reading and the set up of my prod.mdp, these stages should give Coulomb Energy. If you can tell me why or how to fix it, I would greatly appreciate your help. You've defined only a bonded transformation in those stages: bonded-lambdas = 0.0 0.01 0.025 0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 coul-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 Your electrostatic terms remain in state A (lambda = 0) and there is no difference in bonded energies, so the first windows are essentially doing nothing. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Output forces only for select group of atoms
Thanks Justin. This is what I expected but I wanted to make sure I had no other options before I started trying to mess with the code (not one of my strengths). Cheers, Jake From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Tuesday, February 27, 2018 3:18 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Output forces only for select group of atoms On 2/27/18 6:16 PM, Jacob Alan Spooner wrote: > Hi Mark, > > Thank you for your speedy reply. Unfortunately I do not think a rerun will > solve my problem since in that case I will just have to output coordinates of > the entire system at my desired output frequency for the forces, and will > still be generating huge trajectory files. Ideally I would be outputting the > coordinates of the entire system very very infrequently (since I am not > really interested in the coordinates), and outputting the forces for a small > group of atoms very frequently. So in this case I don't think doing a rerun > will save me anyting and will just add a post-processing step. Normally this > would not be an issue but I will be running many simulations of these 25 > atom systems at once, so outputting all the forces (or coordinates) when I > only care about a fraction of them will be a significant problem. > > If anybody else has any ideas about how I could get around this issue I would > be thankful, but I suspect there is no simple solution. Short of modifying the code, the only option is what Mark suggested. GROMACS isn't designed to do what you're asking. -Justin > Best, > Jake > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham > [mark.j.abra...@gmail.com] > Sent: Tuesday, February 27, 2018 1:47 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Output forces only for select group of atoms > > Hi, > > No, but instead see > http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html#re-running-a-simulation > > Mark > > On Tue, Feb 27, 2018 at 10:28 PM Jacob Alan Spooner > wrote: > >> Dear GROMACS users, >> >> I am simulating a fairly large system of about 25 atoms and I want to >> analyze the forces at each output step for only a select group of about 200 >> atoms (and actually only the z component of the force but this is less >> important). My question is whether or not there is a simple way to >> selectively output forces for only my atoms of interest. I will have long >> runs and high output frequency so I would really like to avoid having to >> output force data for the other ~249800 atoms in my system. Any help is >> greatly appreciated! >> >> Thanks, >> Jake Spooner >> -- >> 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Deleting a folder
Hi Justin, Thanks for your answer. So, how can I update a code in GROMACS? Best Ali On Tue, Feb 27, 2018 at 5:25 PM, Justin Lemkul wrote: > > > On 2/27/18 6:23 PM, Ali Ahmed wrote: > >> Hello GROMACS users, >> >> I'm sorry for the crazy things I did. >> I was trying to update electric filed code for magnetic filed >> implementation by adding the cross product term to the force calculation >> equation. unfortunately, I failed and deleted the mdlib folder (GROMACS >> 5.1.2). >> The surprising thing is that GROMAS still applies electric filed. >> My question is, how does GROMACS apply electric field while the code is >> deleted? >> > > Deleting source code has no effect on software that's already installed. > If you try to install again, then your compilation would fail due to > missing files. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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] Deleting a folder
On 2/27/18 10:09 PM, Ali Ahmed wrote: Hi Justin, Thanks for your answer. So, how can I update a code in GROMACS? Modify, compile, install. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] How to use LENNARD JONES 9-6 potential form in GROMACS
Hello List, Can anyone tell me regarding how can i use Lennard Jones 9-6 potential form in GROMACS. Thanks, SK -- 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.
