Hi Justin, Thanks for replying to my query. Please see the error message below of log file. I have user-defined bonded, angle potential which I am providing by supplying tabulated data. I have position restraint also on backbone atoms of the protein that is only in the equilibration steps.
*This is the error message of the log file. * Initializing Domain Decomposition on 8 ranks Dynamic load balancing: off Minimum cell size due to atom displacement: 0.546 nm Initial maximum inter charge-group distances: two-body bonded interactions: 12.145 nm, LJ-14, atoms 11 568 multi-body bonded interactions: 1.124 nm, G96Angle, atoms 3767 3770 Minimum cell size due to bonded interactions: 13.359 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 1.360 nm Estimated maximum distance required for P-LINCS: 1.360 nm Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 16.699 nm The maximum allowed number of cells is: X 0 Y 0 Z 1 ------------------------------------------------------- Program: gmx mdrun, version 2018.6 Source file: src/gromacs/domdec/domdec.cpp (line 6594) MPI rank: 0 (out of 8) Fatal error: There is no domain decomposition for 8 ranks that is compatible with the given box and a minimum cell size of 16.6989 nm Change the number of ranks or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition Please let me know what I can do to rectify it. On Mon, 2 Sep 2019 at 12:25, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: simulation termination problem (Prabir Khatua) > 2. Re: wham analysis (Justin Lemkul) > 3. Re: Domain decomposition error while running coarse grained > simulations on cluster (Justin Lemkul) > 4. Re: mdrun error (Justin Lemkul) > 5. regarding changing the scale from ps to ns (sudha bhagwati) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 1 Sep 2019 12:10:04 -0500 > From: Prabir Khatua <prabir07c...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] simulation termination problem > Message-ID: > < > caobzxoogmnzmky8ddreyhfh7cjm9ycppo3fg6dmoe5fn-mg...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Thanks Justin. The problem has been fixed. > > On Fri, Aug 30, 2019 at 7:31 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 8/29/19 12:31 PM, Prabir Khatua wrote: > > > Hello Gromacs users, > > > > > > I am trying to simulate a system of atom size 3,58,973 in gromacs > 5.1.5. > > > However, my simulation is being terminated in between with the > following > > > error. > > > > > > File input/output error: > > > Cannot rename checkpoint file; maybe you are out of disk space? > > > For more information and tips for troubleshooting, please check the > > GROMACS > > > website at http://www.gromacs.org/Documentation/Errors > > > > > > I did not find any solution with respect to the error I was having in > the > > > mentioned website. What I found was related to memory issue. I do not > > know > > > whether this is the same issue. > > > > The issue is not related to memory, it is (potentially) related to disk > > space. Do you have enough space on the filesystem to write output files? > > This can also happen sometimes when the filesystem blips. There's not > > much you can do about that except complain to your sysadmin about > > integrity of the filesystem. > > > > -Justin > > > > > Please note that I was successfully able to run another simulation of a > > > system having relatively less number of atoms with same script. The run > > > command that I used for the simulation was > > > > > > mpirun -np 48 gmx_mpi mdrun -ntomp 1 -deffnm npt > > > > > > I ran both the simulations on two nodes having 24 cpu cores in each one > > of > > > the nodes. > > > I am also not able to figure out one issue. The log file of the system > > > where the simulation was successfully completed showed > > > > > > Running on 2 nodes with total 48 cores, 48 logical cores, 0 compatible > > GPUs > > > Cores per node: 24 > > > Logical cores per node: 24 > > > Compatible GPUs per node: 0 > > > > > > However, in the unsuccessful case, the log file showed > > > > > > Running on 1 node with total 24 cores, 24 logical cores > > > > > > Thus, it looks like the simulation was running on single node although > I > > > asked it to run on two nodes. I have no idea how to fix this issue. > > Please > > > help me fix this issue or what I am doing wrong. > > > > > > Thanks in advance, > > > > > > Prabir > > > > > > > -- > > ================================================== > > > > 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. > > > > > -- > > *Prabir Khatua* > *Postdoctoral Research Associate* > *Department of Chemistry & Biochemistry* > *University of Oklahoma* > *Norman, Oklahoma 73019* > *U. S. A.* > > > ------------------------------ > > Message: 2 > Date: Sun, 1 Sep 2019 13:21:23 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] wham analysis > Message-ID: <65191dc8-43fd-bc2f-6b9a-20903052d...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 9/1/19 5:35 AM, Negar Parvizi wrote: > > Dear all, > > I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) > for my file which is protein-ligand complex. > > The pulling force was in Y direction. when Umbrella sampling finished, > "Wham" couldn't analysis the data because wham is in z direction.what > should I do now for wham analysis? how can I change it to Y direction? > > I sent message in gromacs comunity , what Justin said: > > "WHAM does not presuppose the axis or vector; it does what you tell it. > If you're referring to the x-axis label in the PMF profile being "z," that > is just a generic (and perhaps imprecise) label that should be changed to > the Greek character xi, per conventional notation." > > I didn't understand it. > > I made a guess based on minimal information. You asserted that you > pulled along y but WHAM indicated the bias was along z. I know that the > default x-axis label in profile.xvg says "z" and it causes confusion. So > I provided the comment that I did. > > However, it is clear from the gmx wham output below that you did *not* > apply a bias along y, as you stated: > > > File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N > Y], (1 dimensions) > > This means your reaction coordinate was the z-axis. > > > So I decided copy the error: > > > > Here is the error: > > > >> Found 25 tpr and 25 pull force files in tpr-files.dat and > pullf-files.dat, respectively > >> Reading 12 tpr and pullf files > >> Automatic determination of boundaries... > >> Reading file umbrella0.tpr, VERSION 5.1.4 (single precision) > >> File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N > Y], (1 dimensions) > > Pull group coordinates not expected in pullx files. > > crd 0) k = 1000 position = 0.840198 > > Use option -v to see this output for all input tpr files > > > >> Reading pull force file with pull geometry distance and 1 pull > dimensions > >> Expecting these columns in pull file: > > 0 reference columns for each individual pull coordinate > > 1 data columns for each pull coordinate > >> With 1 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) > >> Reading file umbrella119.tpr, VERSION 5.1.4 (single precision) > >> Reading file umbrella139.tpr, VERSION 5.1.4 (single precision) > >> Reading file umbrella146.tpr, VERSION 5.1.4 (single precision) > >> Reading file umbrella157.tpr, VERSION 5.1.4 (single precision) > >> Reading file umbrella180.tpr, VERSION 5.1.4 (single precision) > >> Reading file umbrella202.tpr, VERSION 5.1.4 (single precision) > > What happens next? Nothing here says "error," however it looks like your > input files are of an unexpected format. Perhaps you've switched > pullx.xvg and pullf.xvg. As someone else suggested, you can use > pullf.xvg files to get the PMF profile and avoid the issue entirely. > > -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 > > ================================================== > > > > ------------------------------ > > Message: 3 > Date: Sun, 1 Sep 2019 13:22:15 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Domain decomposition error while running > coarse grained simulations on cluster > Message-ID: <71840e02-8747-38b0-d2a0-39da5adbb...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > 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: > > 12.00000 14.00000 18.00000 > > Where I have Protein, membrane (DPPC) and ions. > > I have minimized energy with 16 processor and -rdd option as 2.5. It > worked > > fine but later in NVT simulation, this started giving errors. > > *I am getting the following error without -rdd option when I used 1 node > > and 8 processor per node:* > > Fatal error: > > There is no domain decomposition for 8 ranks that is compatible with the > > given > > box and a minimum cell size of 7.69783 nm > > This minimum cell size is significantly larger than a normal simulation > would require. Do you have restraints or other non-standard interactions > defined? The .log file snippet that describes the DD setup would be > useful for tracking the issue down. > > -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 > > ================================================== > > > > ------------------------------ > > Message: 4 > Date: Sun, 1 Sep 2019 13:23:48 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] mdrun error > Message-ID: <a3299ee2-b645-a330-65f8-3bd18d65a...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 9/1/19 7:02 AM, m g wrote: > > Dear Justin, > There are many other people on this list, and I don't always have answers > :) > > > I'm simulating a system with "wall" for z direction, but I gave this > error in minimization step "software inconsistency error: lost particles > while sorting",.Would you please help me? I used the following?parameter: > > What GROMACS version are you using? CPU or GPU? Does the simulation work > without the walls? You need to provide a lot more diagnostic > information. This is a cryptic error that suggests something very > fundamental is wrong. That also makes it very hard to diagnose. > > If you're not using the latest version of GROMACS, start there. I recall > some bug fixes that may be relevant. If the error is reproducible in > 2019.3, please post a more complete description of what you're doing. > > -Justin > > > integrator? ??? =steep > > > > emtol?????? ?? ?????= 100.0emstep????????????? = 0.01nsteps??????????? > ??? = 5000nstlist?????????? ??? = 1cutoff-scheme?????? = > Verletns_type?????????? ??? = gridrlist?????? ?? ?????= 1.2? ??coulombtype > ?? ?????= PMErcoulomb??? ?? ?????= 1.2vdwtype???????????? = > cutoffvdw-modifier??????? = force-switchrvdw-switch???????? = > 1.0rvdw??????? ? ??????= 1.2????????? ??DispCorr??????????? = nopbc ? > ??????????????=xy? ? ? ? ? ? ? ? ? ??nwall?????????????? = > 2wall_type?????????? = 10-4wall_r_linpot?????? = 1wall_atomtype?????? = ca? > cawall_density??????? = 60? 60wall_ewald_zfac???? = 3ewald-geometry????? = > 3dc > > > > Thanks,Ganj > > > > -- > ================================================== > > 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 > > ================================================== > > > > ------------------------------ > > Message: 5 > Date: Mon, 2 Sep 2019 12:23:25 +0530 > From: sudha bhagwati <sudhabhagw...@gmail.com> > To: gmx-us...@gromacs.org > Subject: [gmx-users] regarding changing the scale from ps to ns > Message-ID: > <CAAjYSb-58-5qEeM+Rq-Yv3yTApA8cb1ktL_DP74n8MoK3j= > 3...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear gmx users, > > I am using the GROAMCS 5.1.4 version. > > ---------------------------------------------------------------------------------------------------------------------------------------- > Running the commands below: > > > *gmx gyrate -s md_0_20.tpr -f md_0_20_noPBC.xtc -o gyrate.xvg -tu ns* > *OR* > *gmx energy -f ie.edr -o interaction_energy.xvg -tu ns* > > > Error while executing commands: > > *Error in user input:* > > *Invalid command-line options Unknown command-line option -tu* > > ---------------------------------------------------------------------------------------------------------------------------------------- > > -tu flag is not working for commands showed above. I want to generate my > plots for nanosecond scale using xmgrace. Could you please help me out with > this issue. I'd be really grateful to you. > > Thank you. > > > -- > Thanks & regards > ~ > Sudha Bhagwati > > > ------------------------------ > > -- > 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. > > End of gromacs.org_gmx-users Digest, Vol 185, Issue 3 > ***************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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