[gmx-users] specific heat calculation using "gmx dos"
Dear all, I am trying to calculate heat capacity of a polymeric system (30k atoms) using gromacs. I tried the classical way from the fluctuation dependent properties using "gmx energy", but the values are not matching experimental values. I want to use "gmx dos" program, but I have some confusions. 1. Does it gives only the quantum corrections in heat capacity, which should be added to the one calculated from 'gmx energy' or Does it gives full heat capacity value including quantum corrections. 2. Should I have to run NVT simulations, run gmx dos, find Cv and the add then calculate Cp, as given in the paper ( J. Chem. Theory Comput. 2012, 8, 61–74), *OR* I can run a NPT simulation and calculate Cp from gmx dos. 3. gmx dos gives the Cp/Cv value in "dos.log" file. but is there any output file to check its convergence. I mean how should I decide, how long the trajectory I should take. 4. Cp can be calculated from the slope of enthalpy vs temp plot (dH/dT) (in a small range of temp), what limitation does this approach have. 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.
[gmx-users] nrexcl value for ions
Dear gromacs users, A very happy new year to all of you. I an trying to simulate LiBr and LiNO3. What will be the value of nrexcl in OPLS itp file for respective cation and anions? I found nrexcl=1 for atomic ions in ions.itp file in gromacs. Again in a tutorial of simulation of Choline Chloride + urea, they have used nrecxl=3 for chloride ion. Here, I am confused about this. Any kind of help will be highly appreciated. Thanks and regards, Dhrubajyoti Maji -- 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] What is the "gen-vel" used for?
I guess I understand what you mean, but could you clarify it further? I usually perform the simulations by the following process: (1) energy minimization (EM); (2) NVT for 1 ns with heavy atom restraints; (3) NPT for 1 ns with heavy atom restrains; (4) production simulation without restraints. To prove repeatability, I think I need to set up several parallel simulations. Could I perform the NPT step for 3 different durations such as 1 ns, 2 ns, 5 ns to get three different velocities at the final frame of the three NPT simulations, and remove the restraints and continue the simulation from these velocities respectively? Thus I will get three production simulations start from different velocities. Or do I need to stop a so-called production simulations (without restraint) at different time points and get three configurations, and repeat the EM, NVT, NPT and production simulation steps for the three configurations respectively to get three independent trajectories? Best regards, Yeping On Fri, Jan 3, 2020 at 9:50 AM Justin Lemkul wrote: > > > On 1/2/20 8:25 PM, Sun Yeping wrote: > > Hello Justin, > > > > Your reply is very helpful. I can understand the first method for proving > > repeatablity: use a different initial configuration. But how to set the > > different initial velocities with the same initial configuration if not > > using the "gen-vel" option in the .mdp file for the production > simulations? > > Again, you don't generate velocities at the outset of a "production" > simulation. You're creating a randomized system that needs to be > re-equilibrated. Hence, velocities are only ever generated at the outset > of the first step of equilibration. Perhaps this is just a discrepancy > in terminology, but one cannot justifiably start a "production" > simulation (i.e. one in which data are collected) from a totally random > state that may not even be stable. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] What is the "gen-vel" used for?
On 1/2/20 8:25 PM, Sun Yeping wrote: Hello Justin, Your reply is very helpful. I can understand the first method for proving repeatablity: use a different initial configuration. But how to set the different initial velocities with the same initial configuration if not using the "gen-vel" option in the .mdp file for the production simulations? Again, you don't generate velocities at the outset of a "production" simulation. You're creating a randomized system that needs to be re-equilibrated. Hence, velocities are only ever generated at the outset of the first step of equilibration. Perhaps this is just a discrepancy in terminology, but one cannot justifiably start a "production" simulation (i.e. one in which data are collected) from a totally random state that may not even be stable. -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] atom moved too far
On 1/2/20 3:02 PM, Christos Deligkaris wrote: thank you Justin. I saw on your umbrella sampling tutorial how to implement the restraints using the pull code. The protocol I used is (if I understand correctly your question): The energy minimization reached the cutoff for maximum force 1000 in 346 steps. My NVT equilibration was 50,000 steps of dt = 0.002 and I used 8 NPT equilibration calculations, each with 31,250 steps of dt=0.002 (total NPT equilibration time 500ps) where I slowly decreased the position restraints on DNA and the small molecule, as well as the harmonic restraint between the two. What are the best temperature coupling groups to use when we are not certain whether the small molecule will spend the entire simulation period physically bound to the macromolecule or whether it will become fully solvated at some point? Is Macromolecule and Non-macromolecule the best option since the small molecule will always (to a small or large extent) interact with water (versus the Macromolecule_and_small_molecule and everything else grouping option)? I doubt there would be a measurable or provable difference between the behaviors of the two setups. -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] What is the "gen-vel" used for?
Hello Justin, Your reply is very helpful. I can understand the first method for proving repeatablity: use a different initial configuration. But how to set the different initial velocities with the same initial configuration if not using the "gen-vel" option in the .mdp file for the production simulations? Best regards, Yeping -- 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] What is the "gen-vel" used for?
On Tue, Dec 31, 2019 at 12:22 PM Justin Lemkul wrote: > > > On 12/30/19 11:11 PM, sunyeping wrote: > > Hello Justin, > > > > Thank you for your reply. > > > > If I need to prove the repeatability of a phenonmenon (such as the > > peptide folding pathway or a conformational transition) in > > simulations, is it reasonable to run the production MD several times > > and each time the simulation is continued for the same NPT > > equilibration? Do I need to introduce centain random factors (if not > > the velocity) in each production simulation? > > > > No, because those aren't independent observations. You're just running > the same .tpr file over and over again, which will diverge slightly for > numerical reasons but these are not true replicate simulations. If you > want to prove repeatability, you need to repeat exactly what you did in > the first case multiple times, with the only difference being either (1) > a different initial configuration or (2) the same configuration with > different initial velocities. The initial condition is what needs to > change, and then you need to equilibrate and perform the simulation the > same way to see if the same behavior arises. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] molecule breakage during minimization
Hello everyone, Before equillibriation I was trying to minimize my protein membrane system. energyminimized.gro file when vizualized in vmd showed few lipid molecules broken. Is it safe to use trjconv to make whole molecule after em or i can proceed with breakage? This is the minimization.mdp file I am using define = -DREST_ON -DSTEP6_0 integrator = steep emtol = 1000.0 nsteps = 5000 nstlist = 10 cutoff-scheme = Verlet rlist = 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 coulombtype = pme rcoulomb= 1.2 ; constraints = h-bonds constraint_algorithm= LINCS -- 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] atom moved too far
thank you Justin. I saw on your umbrella sampling tutorial how to implement the restraints using the pull code. The protocol I used is (if I understand correctly your question): The energy minimization reached the cutoff for maximum force 1000 in 346 steps. My NVT equilibration was 50,000 steps of dt = 0.002 and I used 8 NPT equilibration calculations, each with 31,250 steps of dt=0.002 (total NPT equilibration time 500ps) where I slowly decreased the position restraints on DNA and the small molecule, as well as the harmonic restraint between the two. What are the best temperature coupling groups to use when we are not certain whether the small molecule will spend the entire simulation period physically bound to the macromolecule or whether it will become fully solvated at some point? Is Macromolecule and Non-macromolecule the best option since the small molecule will always (to a small or large extent) interact with water (versus the Macromolecule_and_small_molecule and everything else grouping option)? Best wishes, Christos Deligkaris, PhD Assistant Professor of Physics, University of Southern Indiana SC2220, 8600 University Blvd, Evansville IN, 47712 Office Phone: (812) 228-5056 www.deligkaris.org @DeligkarisGroup On Mon, Dec 30, 2019 at 7:30 AM Justin Lemkul wrote: > > > On 12/30/19 5:34 AM, Christos Deligkaris wrote: > > dear all, > > > > While running my production run of a small molecule noncovalently bound > to > > DNA in water, I got the error: > > > > Step 8921600: > > > > Atom 20338 moved more than the distance allowed by the domain > decomposition > > (0.457738) in direction X > > > > distance out of cell 0.495788 > > > > New coordinates:3.3044.9382.969 > > > > Old cell boundaries in direction X:0.0000.715 > > > > New cell boundaries in direction X:0.0000.709 > > > > > > --- > > > > Program: gmx mdrun, version 2018.1 > > > > Source file: src/gromacs/domdec/domdec.cpp (line 4076) > > > > MPI rank:0 (out of 12) > > > > > > Fatal error: > > > > An atom moved too far between two domain decomposition steps > > > > This usually means that your system is not well equilibrated > > > > The error occured at about time=18 ns. I erased the output files, > > resubmitted the calculation again from the beginning time=0 and in that > > attempt the error appeared at about 16 ns. In both cases it was an atom > of > > a water molecule that moved too far. > > > > I read the "gromacs blow up" webpage and thought maybe the harmonic > > intermolecular constraints I have on the cap base pairs are too strong > for > > the time step of 0.002 so I decreased the time step to 0.001ps and that > > calculation is now at about 60 ns (still running). I also tried using > only > > 6 cores with a step of 0.002 (I used 12 cores in the two failed > > calculations) and that calculation is now at time=50ns (still running). > > > > The energy minimization reached the cutoff for maximum force 1000 in 346 > > steps. My NVT equilibration was 50,000 steps of dt = 0.002 and I used 8 > NPT > > equilibration calculations, each with 31,250 steps of dt=0.002 (total NPT > > equilibration time 500ps) where I slowly decreased the position > restraints > > on DNA and the small molecule, as well as the harmonic restraint between > > the two. > > > > I implemented the harmonic restraint between the small molecule-DNA and > the > > cap base pairs using the following in the topology (just showing one > > example) > > > > [ intermolecular_interactions ] > > > > [ bonds ] > > > > 455 483 6 0.18564 200 > > It is easier to use the pull code to perform the same operation, and is > more likely to be compatible with domain decomposition. > > > For the production run, I use > > > > comm-mode = Linear > > > > nstcomm = 100 > > > > comm-grps = System > > > > > > cutoff-scheme = Verlet > > > > nstlist = 10 > > > > coulombtype = PME > > > > rcoulomb = 1.2 > > > > vdwtype = Cut-off > > > > vdw-modifier = Potential-shift > > > > rvdw = 1.2 > > > > rvdw-switch = 0 > > > > DispCorr = no > > > > tcoupl = nose-hoover > > > > nh-chain-length = 1 > > > > nsttcouple = -1 > > > > tc-grps = DNA_NNK Water_and_ions > > > > tau-t = 0.4 0.4 > > > > ref-t = 300 300 > > > > pcoupl = Parrinello-Rahman > > > > pcoupltype = isotropic > > > > tau-p = 1.0 > > > > ref-p = 1.0 > > > > refcoord-scaling = com > > > > constraints = h-bonds > > > > constraint-algorithm = lincs > > > > I believe SETTLES is included in the TIP3P topology by default so I am > > using that also. > > > > I have run three 50 ns production runs of the small molecule in water > > without any problems (NPT equilibration was done in 1 calculation for > these > > three). > > > > I was surprised that the two failed calculations did not fail at exactly > > the same time step (start with same positions, velocities and solve > > determinist equations of motion). > > Domain decomposition and other optimizations
Re: [gmx-users] Extract LJ-14 energy
On 1/2/20 6:11 AM, Suvardhan Jonnalagadda wrote: Hi, Thanks for the reply. In the log file I could not find any 'LJ14' term, but 'LJ (SR) term is present. My molecule has 17 atoms, and there are 1-4 interactions. 1.) Is the LJ(SR) term not the same as LJ14, in my case, since I have only one molecule? They are different. Depending on how your topology was constructed, LJ(SR) may encompass LJ14, but they are not equivalent. 2.) Also, how to see what 1-4 interactions gromacs has considered for the calculations? When I calculated for the molecule, manually, the 1-4 LJ contribution is mismatching. Use gmx dump on your .tpr file. 1-4 interactions are computed for topologies with nrexcl = 3 and defined [pairs]. If you did not do this, you have no 1-4 energy term, but it will be computed as part of LJ(SR) unless nrexcl > 3. -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] Gromacs 2019 - Ryzen Architecture
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.
[gmx-users] Gromacs 2019 - Ryzen Architecture
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 -- 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] Extract LJ-14 energy
Hi, Thanks for the reply. In the log file I could not find any 'LJ14' term, but 'LJ (SR) term is present. My molecule has 17 atoms, and there are 1-4 interactions. 1.) Is the LJ(SR) term not the same as LJ14, in my case, since I have only one molecule? 2.) Also, how to see what 1-4 interactions gromacs has considered for the calculations? When I calculated for the molecule, manually, the 1-4 LJ contribution is mismatching. Sorry for late response. Thanks and regards, On Sat, 21 Dec, 2019, 7:04 AM Justin Lemkul, wrote: > > > On 12/20/19 6:07 AM, Suvardhan Jonnalagadda wrote: > > Hi, > > Thanks for the reply. > > I have included it and rerun my system. Still problem prevails. > > energrps are not required for LJ 1-4 energies, as these are > intramolecular and energygrps correspond strictly to intermolecular > interaction energies. > > There is no need for enemat, which in any case is not practical to use > enemat, just extract the energies with gmx energy. As Mark said, if your > topology specifies 1-4 interactions, the energy contribution will be > there. If it's not, there are no 1-4 interactions. > > -Justin > > > > > > > On Fri, 20 Dec, 2019, 7:22 AM Bratin Kumar Das, < > 177cy500.bra...@nitk.edu.in> > > wrote: > > > >> Hi > >> You have to mention energygrous in your .mdp file and rerun the > >> simulation. The details you'll get in gromacs protein- ligand complex > >> tutorial. > >> > >> On Thu 19 Dec, 2019, 11:11 PM Suvardhan Jonnalagadda, < > >> j.su.vard...@gmail.com> wrote: > >> > >>> Hi All, > >>> > >>> *"GROMACS: VERSION 4.5.5; Precision: single"* > >>> I have performed an md simulation for 1 time step, on a single molecule > >>> with 17 atoms. I want to calculate all the energies (angle, dihedrals, > >>> bonds, 1-4 interactions), and compare. However, I am not able to get > the > >>> LJ-14 interactions energy from the '*.edr'* file. When i searched in > the > >>> manual, I came across *'gmx enemat'* command. > >>> I gave the following command > >>> > >>> *'gmx enemat -f nvt_single.edr -groups groups.dat -lj14'* > >>> In the groups.dat I have entered the molecule name (as in the *.itp > >>> *file). > >>> > >>> So, the error and warnings I get after the above command are as > follows: > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> *" group 16WARNING! could not find group Coul-SR:C16-C16 (16,16)in > >> energy > >>> fileWARNING! could not find group LJ-SR:C16-C16 (16,16)in energy > >>> fileWARNING! could not find group LJ-14:C16-C16 (16,16)in energy > fileWill > >>> select half-matrix of energies with 0 elementsLast energy frame read 0 > >>> time0.000Will build energy half-matrix of 17 groups, 0 > >>> elements, over 1 framesSegmentation fault (core dumped) "* > >>> Is this a bug? or am I missing something? > >>> Also, what does 'LJ(SR)' term in the energies include? In my case, I > have > >>> only one molecule. So, what does this LJ short range include? > >>> > >>> Thank you, > >>> > >>> Best regards, > >>> Vardhan > >>> -- > >>> 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 > 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] lifetime of hydrogen bond
Thank you for your suggestion. - Message from David van der Spoel - Date: Thu, 2 Jan 2020 08:28:17 +0100 From: David van der Spoel Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] lifetime of hydrogen bond To: gmx-us...@gromacs.org Den 2020-01-02 kl. 07:47, skrev sp...@iacs.res.in: Dear all I want to calculate the hydrogen bond lifetime of a dynamic hydrogen bond which stays for say 10 ns (as I have saved the trajectory with 10 ps interval). I am trying to calculate the lifetime of this hydrogen bond by gmx hbond command gmx hbond -f traj_nopbc.trr -s md.tpr -n index.ndx -num hbond_G4_N3_131_N3H4.xvg -dist dist_G4_N3_131_N3H4.xvg -ang ang_G4_N3_131_N3H4.xvg -life life_G4_N3_131_N3H4.xvg Its give me a "uninterrupted hydrogen bond lifetime" plot which stays for 200 ps. I cannot understand the meaning of this plot. How to explain this 200 ps lifetime? Thanks sunipa The -life option does not give you a meaningful answer since it is sensitive to small fluctuations. My oldpaper in J. Phys. Chem. B 110 pp. 4393-4398 (2006) explains it in detail. You can rerun without -life and with the -ac flag. -- 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 visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. - End message from David van der Spoel - -- 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.
