Re: [gmx-users] Domain decomposition error while running coarse grained simulations on cluster

> > Here's your problem. You have pairs defined that are in excess of 12 nm, > but they are assigned to a 1-4 interaction, so atoms that should be > separated by three bonds. The user-defined potential shouldn't matter > here unless you've added [pairs] to the topology. > > I see your point. What

Re: [gmx-users] Domain decomposition error while running coarse grained simulations on cluster

chemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Message: 3 Date: Sun, 1 Sep 2019 13:22:15 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re

Re: [gmx-users] Domain decomposition error while running coarse grained simulations on cluster

pull groups, expect 2 columns (including the time column) > >> Reading file umbrella71.tpr, VERSION 5.1.4 (single precision) > >> Reading file umbrella98.tpr, VERSION 5.1.4 (single precision) > >> Reading file umbrella111.tpr, VERSION 5.1.4 (single precision) >

Re: [gmx-users] Domain decomposition error while running coarse grained simulations on cluster

On 9/1/19 5:44 AM, Avijeet Kulshrestha wrote: Hi all, I am running martini coarse-grained simulation with 15 fs of time step in gromacs 2018.6. I have 25859 number of atoms and my box size is: 12.0 14.0 18.0 Where I have Protein, membrane (DPPC) and ions. I have minimized energy

[gmx-users] Domain decomposition error while running coarse grained simulations on cluster

Hi all, I am running martini coarse-grained simulation with 15 fs of time step in gromacs 2018.6. I have 25859 number of atoms and my box size is: 12.0 14.0 18.0 Where I have Protein, membrane (DPPC) and ions. I have minimized energy with 16 processor and -rdd option as 2.5. It

Re: [gmx-users] domain decomposition error >60 ns into simulation on a specific machine

Hi Mark, To my knowledge, she's not using CHARMM-related FF's at all -- I think she is using Amber03 (Alyssa, correct me if I'm wrong). Visually and RSMD-wise the trajectory looks totally normal, but is there something specific I should be looking for in the trajectory, either visually or

Re: [gmx-users] domain decomposition error >60 ns into simulation on a specific machine

Hi, What does the trajectory look like before it crashes? We did recently fix a bug relevant to simulations using CHARMM switching functions on GPUs, if that could be an explanation. We will probably put out a new 2018 version with that fix next week (or so). Mark On Thu., 14 Feb. 2019, 20:26

[gmx-users] domain decomposition error >60 ns into simulation on a specific machine

Hi all, My student is trying to do a fairly straightforward MD simulation -- a protein complex in water with ions with *no* pull coordinate. It's on an NVidia GPU-based machine and we're running gromacs 2018.3. About 65 ns into the simulation, it dies with: "an atom moved too far between two

Re: [gmx-users] domain decomposition error

Hi, The implicit solvent support got a bit broken between 4.5 and 4.6, and nobody has yet worked out how to fix it, sorry. If you can run with 1 cpu, do that. Otherwise, please use GROMACS 4.5.7. Mark On Mon, Jun 18, 2018 at 9:21 AM Chhaya Singh wrote: > I am running a simulation having

[gmx-users] domain decomposition error

I am running a simulation having protein in implicit solvent using amber ff99sb forcefield and gbsa as solvent . I am not able to use more than one cpu. It always gives domain decomposition error if i use more than one cpu. when i tried running using one cpu then it gave me this error : "Fatal

Re: [gmx-users] Domain decomposition error with -rerun

Check the trajectories before and after conversion and make sure that there are no pbc effect, if so fix it. Or do the analysis with the avaible trajectories(may be in VMD with tcl scripts). -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Domain decomposition error with -rerun

Thanks for the reply Mark. On Sat, Apr 28, 2018 at 4:32 PM, Mark Abraham wrote: > Hi, > > Clearly the conversion tool did not produce a file that conforms to the > requirements GROMACS has for specifying periodic boxes. That may not work > well even if you'd run mdrun

Re: [gmx-users] Domain decomposition error with -rerun

Hi, Clearly the conversion tool did not produce a file that conforms to the requirements GROMACS has for specifying periodic boxes. That may not work well even if you'd run mdrun without domain decomposition because the periodicity may not be understood correctly. Find out what was going on and

Re: [gmx-users] Domain decomposition error with -rerun

Yes.. I used VMD for conversion... On Sat, Apr 28, 2018 at 12:50 PM, RAHUL SURESH wrote: > Hi > > Sounds strange to my little knowledge. How I would justify is, it may be > due to the conversion from NAMD [dcd] to Gromacs profile [trr] though not > sure. > > So you have

Re: [gmx-users] Domain decomposition error with -rerun

Hi Sounds strange to my little knowledge. How I would justify is, it may be due to the conversion from NAMD [dcd] to Gromacs profile [trr] though not sure. So you have converted the file format using VMD? On Sat, Apr 28, 2018 at 12:26 PM, Sahithya S Iyer wrote: > Hi, > >

Re: [gmx-users] Domain decomposition error with -rerun

Hi, Thanks for the reply. I am only doing a rerun of a trajectory that has already evolved without any dynamic load balancing problems. -rerun only recalculates energies right. I don't understand why the same trajectory is giving decomposition error now. On Sat, Apr 28, 2018 at 12:11 PM, RAHUL

Re: [gmx-users] Domain decomposition error with -rerun

Hi. That indicates a problem with dynamic load balancing. Try to build different sizes of the box. On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer wrote: > Hi, > > I am trying to calculate interaction between specific residues using gmx > mdrun -rerun flag. The trajectory

[gmx-users] Domain decomposition error with -rerun

Hi, I am trying to calculate interaction between specific residues using gmx mdrun -rerun flag. The trajectory was in a dcd format, which I converted to a trr file. I get the following error - Domain decomposition has not been implemented for box vectors that have non-zero components in

Re: [gmx-users] Domain decomposition error

Well, I do not do anything special when preparing this system compared to other systems that do not show this issue. I have carefuly inspected my system and I know what is wrong. I did some manipulations to PDB file due to missing fragment of residue and accidentally put NZ atom of Lysine like

Re: [gmx-users] Domain decomposition error

On 4/15/18 9:29 AM, Dawid das wrote: Dear Gromacs Users, I run numerous MD simulations for similar systems of protein in water box and for only one system I encounter error: *Fatal error:There is no domain decomposition for 4 ranks that is compatible with the givenbox and a minimum cell

[gmx-users] Domain decomposition error

Dear Gromacs Users, I run numerous MD simulations for similar systems of protein in water box and for only one system I encounter error: *Fatal error:There is no domain decomposition for 4 ranks that is compatible with the givenbox and a minimum cell size of 3.54253 nmChange the number of

Re: [gmx-users] Domain decomposition error

On 5/18/17 5:59 AM, Kashif wrote: I got this error every time when I try to simulate one of my protein-ligand complex. --- Program mdrun, VERSION 4.6.6 Source code file: /root/Documents/gromacs-4.6.6/src/mdlib/pme.c, line: 851 Fatal error:

[gmx-users] Domain decomposition error

I got this error every time when I try to simulate one of my protein-ligand complex. --- Program mdrun, VERSION 4.6.6 Source code file: /root/Documents/gromacs-4.6.6/src/mdlib/pme.c, line: 851 Fatal error: 1 particles communicated to PME node

[gmx-users] domain decomposition error- ------

Dear all gromacs users, I have seen in mail archive this domain decomposition error can be avoided with less number of processor, but how to find the suitable number of processor required? here is the log file. ​​https://drive.google.com/file/d/0Bzs8lO6WJxD9alRTYjFaMjBTT2c/ view?usp=sharing --

[gmx-users] domain decomposition error

Dear all gromacs users, I have seen in mail archive this domain decomposition error can be avoided with less number of processor, but how to find the suitable number of processor required? here is the log file. ​​ https://drive.google.com/file/d/0Bzs8lO6WJxD9alRTYjFaMjBTT2c/view?usp=sharing --

Re: [gmx-users] domain decomposition Error

" <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org > Sent: Tuesday, March 7, 2017 4:25:12 AM > Subject: Re: [gmx-users] domain decomposition Error > > Hi, > > Exactly. NVT not exploding doesn't mean it's ready for NpT, particularly if > the volume is just wron

Re: [gmx-users] domain decomposition Error

raham" <mark.j.abra...@gmail.com> To: gmx-us...@gromacs.org Sent: Tuesday, March 7, 2017 4:25:12 AM Subject: Re: [gmx-users] domain decomposition Error Hi, Exactly. NVT not exploding doesn't mean it's ready for NpT, particularly if the volume is just wrong, or you try to use parrinello

Re: [gmx-users] domain decomposition Error

acs.org > Sent: Tuesday, March 7, 2017 2:32:46 AM > Subject: Re: [gmx-users] domain decomposition Error > > Hi, > > There's good advice for this problem at think link that was suggested in > the error message: http://www.gromacs.org/Documentation/Errors. Probably > your box volume o

Re: [gmx-users] domain decomposition Error

gromacs.org Sent: Tuesday, March 7, 2017 2:32:46 AM Subject: Re: [gmx-users] domain decomposition Error Hi, There's good advice for this problem at think link that was suggested in the error message: http://www.gromacs.org/Documentation/Errors. Probably your box volume or NpT protocol need some

Re: [gmx-users] domain decomposition Error

Hi, There's good advice for this problem at think link that was suggested in the error message: http://www.gromacs.org/Documentation/Errors. Probably your box volume or NpT protocol need some attention. Mark On Tue, 7 Mar 2017 06:23 shweta singh wrote: > Thank you ! >

Re: [gmx-users] domain decomposition Error

Thank you ! On Tue, Mar 7, 2017 at 9:47 AM, MRINAL ARANDHARA < arandharamri...@iitkgp.ac.in> wrote: > I am trying to run a lipid bilayer simulation but during the npt > equillibration step I am getting the following error > "1 particles communicated to PME rank 6 are more than 2/3 times the >

[gmx-users] Domain Decomposition Error

I am trying to run a lipid bilayer simulation but during the npt equillibration step I am getting the following error "1 particles communicated to PME rank 6 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y" I have successfully run the

[gmx-users] domain decomposition Error

I am trying to run a lipid bilayer simulation but during the npt equillibration step I am getting the following error "1 particles communicated to PME rank 6 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y" I have successfully run the

Re: [gmx-users] domain decomposition error in the energy minimization step

Hi Qasim, > On 12 Jan 2017, at 20:22, qasimp...@gmail.com wrote: > > Hi Carsten, > > I think I couldn't clearly explain the protocol that I follow. Sorry for > that. Firstly, I do the EM, nvt (100 ps), npt (100 ps) and md (100 ns) steps > for the equilibrium. In all those steps I use the

Re: [gmx-users] domain decomposition error in the energy minimization step

Hi Carsten, I think I couldn't clearly explain the protocol that I follow. Sorry for that. Firstly, I do the EM, nvt (100 ps), npt (100 ps) and md (100 ns) steps for the equilibrium. In all those steps I use the below free energy parameters for the forward state: free-energy = yes init-lambda

Re: [gmx-users] domain decomposition error in the energy minimization step

Hi Qasim, > On 11 Jan 2017, at 20:29, Qasim Pars wrote: > > Dear Carsten, > > Thanks. The forward state simulations works properly with mdrun -ntmpi 8 > -ntomp 2 or mdrun -ntmpi 4 -ntomp 4 as you suggested. > For the backward state GROMACS still gives too many lincs

Re: [gmx-users] domain decomposition error in the energy minimization step

Dear Carsten, Thanks. The forward state simulations works properly with mdrun -ntmpi 8 -ntomp 2 or mdrun -ntmpi 4 -ntomp 4 as you suggested. For the backward state GROMACS still gives too many lincs warning error with those mdrun commands in the md step, indicating the system is far from

Re: [gmx-users] domain decomposition error in the energy minimization step

Dear Qasim, those kinds of domain decomposition 'errors' can happen when you try to distibute an MD system among too many MPI ranks. There is a minimum cell length for each domain decomposition cell in each dimension, which depends on the chosen cutoff radii and possibly other inter-atomic

[gmx-users] domain decomposition error in the energy minimization step

Dear users, I am trying to simulate a protein-ligand system including ~2 atoms with waters using GROMACS-2016.1. The protocol I tried is forward state for the free energy calculation. The best ligand pose used in the simulations was got by AutoDock. At the beginning of the simulation GROMACS

Re: [gmx-users] Domain decomposition error tied to free energy perturbation

On Fri, Mar 18, 2016 at 7:47 AM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > > Message: 4 > Date: Fri, 18 Mar 2016 07:46:48 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Domain de

[gmx-users] Domain decomposition error tied to free energy perturbation

Hello, I have been attempting to carry out some free energy calculations, but to verify the sanity of my parameters, I decided to test them on a structure I knew to be stable -- the lysozyme from Lemkul's lysozyme in water tutorial. I chose the L75A mutation because it is out on the surface to

Re: [gmx-users] Domain decomposition error tied to free energy perturbation

On 3/17/16 8:21 PM, Ryan Muraglia wrote: Hello, I have been attempting to carry out some free energy calculations, but to verify the sanity of my parameters, I decided to test them on a structure I knew to be stable -- the lysozyme from Lemkul's lysozyme in water tutorial. I chose the L75A

Re: [gmx-users] Domain decomposition error

I think i've just found my mistake. Thank you so much again. Khatnaa    On Friday, 30 October 2015, 18:55, Justin Lemkul wrote: On 10/30/15 7:09 AM, badamkhatan togoldor wrote: > Thank you Justin. >> The better question is why you're trying to decouple an entire

Re: [gmx-users] Domain decomposition error

On 10/30/15 7:09 AM, badamkhatan togoldor wrote: Thank you Justin. The better question is why you're trying to decouple an entire protein; that is extremely impractical and unlikely to be useful. Did i do that? then it's my mistake of less knowledge off that. How i fix that? Khatnaa

Re: [gmx-users] Domain decomposition error

Thank you Justin.  >The better question is why you're trying to decouple an entire protein; that >is  >extremely impractical and unlikely to be useful. Did i do that? then it's my mistake of less knowledge off that. How i fix that?      Khatnaa On Friday, 30 October 2015, 1:14, Justin

[gmx-users] Domain decomposition error

Dear GMX Users, I am simulating a free energy of a protein chain_A in water by parallel. Then i got domain decomposition error in mdrun.  Will use 15 particle-particle and 9 PME only ranksThis is a guess, check the performance at the end of the log file

[gmx-users] domain decomposition error

Dear users During energy minimization for IL-water system in a box size of 4.7x4.7x9.4 with432 BMIMTF2N and 3519 water molecules, the following error is written in the md.log file. Initializing Domain Decomposition on 144 nodes Dynamic load balancing: no Will sort the charge groups at every

Re: [gmx-users] domain decomposition error

Hi SMA, It says you have bonds over large distances. Check the structure/topology/setup. Cheers, Tsjerk On Oct 27, 2015 08:02, "Musharaf Ali" wrote: > Dear users > During energy minimization for IL-water system in a box size of 4.7x4.7x9.4 > with432 BMIMTF2N and 3519

Re: [gmx-users] Domain Decomposition error with Implicit Solvent

Thank you Mark for the reply. We are not sure about it either as it worked when we started the simulation again using the cpt file and also there was no issue when we did the same simulation using (links algorithm) constraints. Thanks, Siva On Jul 23, 2014, at 4:20 PM, Mark Abraham

Re: [gmx-users] Domain Decomposition error with Implicit Solvent

On Mon, Jul 21, 2014 at 3:48 PM, Siva Dasetty sdas...@g.clemson.edu wrote: Dear All, I am running simulations of BMP2 protein and graphite sheet using implicit solvent model (mdp file is pasted below). The graphite atoms are frozen in the simulation and BMP2 is free to translate. I got an

[gmx-users] Domain Decomposition error with Implicit Solvent

Dear All, I am running simulations of BMP2 protein and graphite sheet using implicit solvent model (mdp file is pasted below). The graphite atoms are frozen in the simulation and BMP2 is free to translate. I got an error Step 1786210: The domain decomposition grid has shifted too much in the

[gmx-users] Domain Decomposition error with Implicit Solvent

Dear All, I am running simulations of BMP2 protein and graphite sheet using implicit solvent model (mdp file is pasted below). The graphite atoms are frozen in the simulation and BMP2 is free to translate. I got an error Step 1786210: The domain decomposition grid has shifted too much in the

[gmx-users] Domain Decomposition error with Implicit Solvent

Dear All, I am running simulations of BMP2 protein and graphite sheet using implicit solvent model (mdp file is pasted below). The graphite atoms are frozen in the simulation and BMP2 is free to translate. I got an error Step 1786210: The domain decomposition grid has shifted too much in the

[gmx-users] Domain decomposition error with implicit solvent

Dear All, I am running simulations of BMP2 protein and graphite sheet using implicit solvent model (mdp file is pasted below). The graphite atoms are frozen in the simulation and BMP2 is free to translate. I got an error Step 1786210: The domain decomposition grid has shifted too much in the