[gmx-users] Enthalpy calculation in NPT ensemble
Dear GROMACS users,
I am working on simulating a glycine crystal using GAFF force field with CNDO
point charges in an NPT ensemble. I want to calculate the enthalpy and Cp of
the crystal. However, the list that comes up following gmx energy command does
not include the enthalpy or PV options, as it would normally do for NPT
simulations. Does this mean that the simulation does not exhibit NPT behavior?
I believe that this is not the case, since upon inspection of the temperature
and pressure values, I found that they are both constant (within statistical
error) throughout the simulation. What may be the cause of this? The following
are some of my input parameters:
cutoff-scheme = Verlet
nstlist= 40
ns-type= Grid
pbc= xyz
verlet-buffer-tolerance= 0.005
rlist = 1.4
coulombtype= PME
coulomb-modifier = Potential-shift
rcoulomb-switch= 0
rcoulomb = 1.4
rvdw = 1.4
DispCorr = EnerPres
table-extension= 1
fourierspacing = 0.12
pme-order = 4
tcoupl = V-rescale
nsttcouple = 10
pcoupl = Berendsen
pcoupltype = Anisotropic
nstpcouple = 10
tau-p = 2
compressibility (3x3):
compressibility[0]={ 4.5e-05, 4.5e-05, 4.5e-05}
compressibility[1]={ 4.5e-05, 4.5e-05, 4.5e-05}
compressibility[2]={ 4.5e-05, 4.5e-05, 4.5e-05}
ref-p (3x3):
ref-p[0]={ 1.0e+00, 1.0e+00, 1.0e+00}
ref-p[1]={ 1.0e+00, 1.0e+00, 1.0e+00}
ref-p[2]={ 1.0e+00, 1.0e+00, 1.0e+00}
refcoord-scaling = COM
Any input would be greatly appreciated. Thanks in advance.
Pelin Su Bulutoglu
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[gmx-users] Cannot compute velocity of COM of a group of atoms
Dear all, I have simulated a system of DNA and Protein, and I want to calculate the velocity of the center of mass of protein as a function of time. So I used the following command : gmx traj -f traj_comp.trr -s md_run-E-Field.tpr -n index.ndx -ov test-vel.xvg -com I have pasted below the file that it generates : # GROMACS: gmx traj, VERSION 5.0.6 # Executable: /applic/applications/GROMACS/5.0.6/bin/gmx # Library dir: /applic/applications/GROMACS/5.0.6/share/gromacs/top # Command line: # gmx traj -f traj_comp.trr -s md_run-E-Field.tpr -n index.ndx -ov test-vel.xvg -com # gmx is part of G R O M A C S: # # Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm # @title "Center of mass velocity" @xaxis label "Time (ps)" @yaxis label "Velocity (nm/ps)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Protein X" @ s1 legend "Protein Y" @ s2 legend "Protein Z" "test-vel.xvg" 24L, 731C 24,1 Bot So it doesn't have the velocities. Is it due to the fact that in my .mdp file, I had set nstvout = 0 ? I have pasted below the initial part of my .mdp file title = NVT equilibration with position restraint on all solute (topology modified) ; Run parameters integrator = md; leap-frog integrator nsteps = 500 ; 1 * 50 = 500 ps ;nsteps = 5000 dt = 0.02 ; 1 fs ; Output control nstxout = 0 ; save coordinates every 10 ps nstvout = 0 ; save velocities every 10 ps nstcalcenergy = 50 nstenergy = 1000 ; save energies every 1 ps nstxtcout = 2500 ;nstxout-compressed = 5000 ; save compressed coordinates every 1.0 ps ; nstxout-compressed replaces nstxtcout ;compressed-x-grps = System ; replaces xtc-grps nstlog = 1000 ; update log file every 1 ps ; Bond parameters continuation= no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained ;lincs_iter = 2 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy Is there a way I can still compute the velocities, or do I need to run the simulation again, putting nstvout = nsteps ? I would highly appreciate any help. Thank you very much, Regards, Arnab -- 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] NVIDIA CUDA Alanine Scanning
Hi, Yes, you can use CUDA acceleration, and FEP does work, try to keep feature-parity between the GPU-accelerated and non-accelerated modes of GROMACS. Can't comment in depth about GMXPBSA, they may not have full support for newer releases from what a brief look at their mailing list shows. Regarding FEP, the caveat is that not all tasks can be offloaded to the GPU, the free energy short-range computation itself as well as the entire PME computation has to run on the CPU, and therefore such runs may not perform on some hardware as efficiently as it would without FEP. That is especially true if you have very few CPU cores per GPU. However note that the GROMACS CPU code is rather well tuned so the using the CPU for some (or all) is not cripplingly slow as you might have seen with other codes. -- Szilárd On Thu, Jul 26, 2018 at 5:28 PM Matthew Kenney < matthew.ken...@cellsignal.com> wrote: > Hi everyone, > > I am attempting to find a means to perform Alanine scanning mutagenesis > with CUDA acceleration, but have yet to find a free/open-source option. > AMBER and Schrödinger appear to be the only options available for these > calculations on CUDA, and I'd like to avoid the hefty industry licences for > these programs. Hopefully, GROMACS is the solution. > > Does anyone know if the tool GMXPBSA, or Free Energy Perturbation (FEP) > calculations happen to support CUDA? I ask because many programs I've > looked at claim overall CUDA support (ex: NAMD/VMD) but do not support FEP > and certain other types of calculations on CUDA. Any help is much > appreciated. Thanks! > > Best, > Matt > > -- > This message contains information which may be confidential and/or > protected by attorney-client privilege. Unless you are the addressee, you > may not use, copy or disclose to anyone this message or any information > contained in this message. If you have received this message in error, > please send me an email and delete this message. Thank you. > -- > 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] periodic-molecules = yes and movie
Thanks. On Tue, Aug 7, 2018 at 8:30 AM Justin Lemkul wrote: > > > On 8/7/18 8:23 AM, Alex wrote: > > Dear all, > > In the simulation of a system in which there is slab, I did not use > > "periodic-molecules > > = yes" unfortunately, hence I can not make a good movie out of the > > This is not some magic setting that will make nice movies. Note that a > "periodic molecule" is different from just normal PBC. Periodic > molecules are "infinite" molecules like sheets, nanotubes, etc. that > have bonds between central image atoms and periodic copies of atoms. If > you needed such a setting and did not use it, likely your simulation > would have collapsed. No, the simulation did not blow up and worked nicely. As far as I understood and in general the periodic-molecule = yes should be used when a surface is connected to it's image in the neighbouring cell, mine is silica slab, and if the the slab is defined only by non-bonded interaction like most of the metallic slab the periodic molecule = NO should work finely in spite of being infinite. > > trajectory using VMD, the slab move during the movie. The simulation is > > around 300 ns and I do not want to just waste the CPU time, so, I wonder > if > > there is still any solution for that to make a good movie out of that > > trajectory? > > Many of the normal trjconv routines could likely help here. Accounting > for PBC effects like these is a standard first step in post-processing > any trajectory. > Actually what I see is the result of two below comments applied over the > initial trajectory: > gmx_mpi trjconv -f prd.xtc -s eql1.gro -o nojump-skip-30-prd.xtc -center -pbc nojump -n input/index.ndx -tu ns -skip 30 < choice : salb, system gmx_mpi trjconv -f nojump-skip-30-prd.xtc -s prd.tpr -o nopbc-nojump-skip-30-prd.xtc -center -pbc whole -ur compact -n input/index.ndx -tu ns < choice : salb, system Regards, Alex > -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.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] GMXRC removes trailing colon from existing MANPATH
Hi, Can you please submit your change to gerrit.gromacs.org -- and perhaps it's best if you also file an issue on redmine.gromacs.org with your brief description you posted here? Thanks, -- Szilárd On Fri, Jul 27, 2018 at 2:28 PM Peter Kroon wrote: > Hi all, > > I noticed that sourcing GMXRC removes any trailing colons from a set > MANPATH environment variable. This colon *is* syntactically significant, > and removing it causes `mandb` to ignore /etc/manpath.config instead of > appending that file: > > > > unset MANPATH > > export MANPATH=/opt/puppetlabs/puppet/share/man: > > # Note the trailing colon > > echo $MANPATH > /opt/puppetlabs/puppet/share/man: > > mandb > mandb: warning: $MANPATH set, appending /etc/manpath.config > ... > > source /usr/local/gromacs-2018.1/bin/GMXRC > > # No more trailing colon > > echo $MANPATH > > /usr/local/gromacs-2018.1/share/man:/opt/puppetlabs/puppet/share/man > mandb: warning: $MANPATH set, ignoring /etc/manpath.config > ... > > Should I also report this on redmine, or is this sufficient? > > > Peter > > > -- > 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] gromacs with mps
Hi, It does sound like a CUDA/MPS setup issue, GROMACS uses relatively small amount of GPU memory, so unless you are using a very skinny GPU or a very large input, it's most likely not a GROMACS issue. BTW, have you made sure that your GPUs are not in process-exclusive mode? Cheers, -- Szilárd On Fri, Jul 27, 2018 at 9:21 PM Mahmood Naderan wrote: > Hi > Has anyone run gmx_mpi with MPS? Even with small input files (which are > working fine when MPS is turned off), I get out of memory error from the > GPU device. > Don't know if there is a bug inside cuda or gromacs. I see some other > related topics for other programs. So, it sound like a cuda problem. > If you have worked with MPS, please let me know. > > Regards, > Mahmood > -- > 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] Issue with regression test.
Hi, Can you share the directory of the failed test, i.e. regressiontests/complex/nbnxn_vsite? Can you check running the regressiontests manually using 1/2/4 ranks, e.g. perl gmxtest.pl complex -nt 1 -- Szilárd On Wed, Aug 1, 2018 at 12:49 PM Raymond Arter wrote: > Dear All, > > I'm building Gromacs 2018.2 and I've run in to a small issue that I would > like feed back on. > > One of the regression tests fails with the following entered in to the log > file. > > > Mdrun cannot use the requested (or automatic) number of ranks, retrying > with 8. > > Abnormal return value for ' gmx mdrun-nb cpu -notunepme >mdrun.out > 2>&1' was 1 > Retrying mdrun with better settings... > > Abnormal return value for ' gmx mdrun -ntmpi 12 -notunepme >mdrun.out > 2>&1' was 1 > Retrying mdrun with better settings... > > Abnormal return value for ' gmx mdrun -ntmpi 6 -notunepme >mdrun.out > 2>&1' was -1 > FAILED. Check mdrun.out, md.log file(s) in nbnxn_vsite for nbnxn_vsite > Re-running orientation-restraints using CPU-based PME > Re-running pull_geometry_angle using CPU-based PME > Re-running pull_geometry_angle-axis using CPU-based PME > Re-running pull_geometry_dihedral using CPU-based PME > > > However, on the advice of a colleague I run the following command in the > directory: > > gmx mdrun -ntmpi 4 -notunepme > > And got the following result: > > > Reading file topol.tpr, VERSION 2018.2 (single precision) > Non-default thread affinity set, disabling internal thread affinity > Can not increase nstlist because verlet-buffer-tolerance is not set or used > > Using 4 MPI threads > Using 3 OpenMP threads per tMPI thread > > On host ** 4 GPUs auto-selected for this run. > Mapping of GPU IDs to the 4 GPU tasks in the 4 ranks on this node: > PP:0,PP:1,PP:2,PP:3 > > Back Off! I just backed up traj.trr to ./#traj.trr.1# > > Back Off! I just backed up ener.edr to ./#ener.edr.1# > starting mdrun 'Protein' > 20 steps, 0.1 ps. > > step 20 Turning on dynamic load balancing, because the performance loss due > to load imbalance is 3.3 %. > > Writing final coordinates. > > Back Off! I just backed up confout.gro to ./#confout.gro.1# > > Dynamic load balancing report: > DLB was turned on during the run due to measured imbalance. > Average load imbalance: 13.0%. > The balanceable part of the MD step is 25%, load imbalance is computed > from this. > Part of the total run time spent waiting due to load imbalance: 3.3%. > Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 > % Y 0 % > > NOTE: 6 % of the run time was spent in domain decomposition, > 17 % of the run time was spent in pair search, > you might want to increase nstlist (this has no effect on accuracy) > >Core t (s) Wall t (s)(%) >Time:1.9320.161 1200.0 > (ns/day)(hour/ns) > Performance: 56.3370.426 > > > Is this just a problem with the regression test and the build of Gromacs is > fine, or > is there a problem with the build I have done? > > Thanks in advance. > > R. > -- > 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] periodic-molecules = yes and movie
On 8/7/18 8:23 AM, Alex wrote: Dear all, In the simulation of a system in which there is slab, I did not use "periodic-molecules = yes" unfortunately, hence I can not make a good movie out of the This is not some magic setting that will make nice movies. Note that a "periodic molecule" is different from just normal PBC. Periodic molecules are "infinite" molecules like sheets, nanotubes, etc. that have bonds between central image atoms and periodic copies of atoms. If you needed such a setting and did not use it, likely your simulation would have collapsed. trajectory using VMD, the slab move during the movie. The simulation is around 300 ns and I do not want to just waste the CPU time, so, I wonder if there is still any solution for that to make a good movie out of that trajectory? Many of the normal trjconv routines could likely help here. Accounting for PBC effects like these is a standard first step in post-processing any trajectory. -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.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] Too few cells to run on multiple cores
Hi, The domain decomposition has certain algorithmic limits that you can relax, but as you notice that comes at the cost of deteriorating load balance -- and at a certain point it might come at the cost of simulations aborting mid-run (if you make -rdd too large). More load imbalance does not necessarily mean less performance, so if your only way of using more cores is to "squeeze out" more domains of your system, as long as you get more performance, that may be fine. However, instead of trying to squeeze out more domains, you can actually use multiple CPU cores per domain; see the -ntomp option and examples here: http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html For instance, in your case you could use 4 threads per MPI rank and with a 3x2x2 decoposition you'd get 12 domains x 4 threads = 48 threads total. A few more tips: - your original cell size limit was due to bonded interactions, so tweaking LINCS would not help with that - you can also try to use separate PME ranks and by doing that some cores will be reserved for PME work and the domain-decomposition may be stretched a bit less, e.g.: -ntmpi 24 -npme 6 -ntomp 2 will give a 3x3x2 decomposition. the success of this split will of course depend on the PME load in the system (which is estimated to be very high -- are you using some non-default settings?) Cheers, -- Szilárd On Tue, Aug 7, 2018 at 1:52 PM Adrian Devitt-Lee wrote: > Hi, > > I'm having an issue using mdrun in parallel on 48 cores. I'm trying to > figure out which options I can include in the .mdp file to increase the > number of cells in my system. The full error message is: > > Initializing Domain Decomposition on 48 ranks > Dynamic load balancing: auto > Will sort the charge groups at every domain (re)decomposition > Initial maximum inter charge-group distances: > two-body bonded interactions: 1.368 nm, LJC Pairs NB, atoms 2123 2152 > multi-body bonded interactions: 0.428 nm, Proper Dih., atoms 1105 1113 > *Minimum cell size due to bonded interactions: 1.505 nm* > Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 0.219 nm > Estimated maximum distance required for P-LINCS: 0.219 nm > Guess for relative PME load: 0.65 > Using 0 separate PME ranks, as guessed by mdrun > Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 > > *Optimizing the DD grid for 48 cells with a minimum initial size of 1.881 > nmThe maximum allowed number of cells is: X 3 Y 3 Z 3* > > --- > Program mdrun_mpi, VERSION 5.1 > Source code file: > /work/y07/y07/gmx/5.1-phase2/source/src/gromacs/domdec/domdec.cpp, line: > 6969 > > Fatal error: > There is no domain decomposition for 48 ranks that is compatible with the > given box and a minimum cell size of 1.88133 nm > > > I understand the problem -- the system wants to assign one core to each > grid cell, but there are only 3x3x3 = 27 cells. I don't know what I can do > to fix this problem. The system is a solvated protein bound to a ligand in > a ~15 nm box, and it has > 40,000 atoms. I have tried changing the > lincs-order and fourier-spacing to no avail. > > I was able to get the system to run by adding the following flags to mdrun: > -rdd 1.2 -dds 0.9 > > But when I did this, the force imbalance went to > 140%, and 10-30% of the > cpu time was lost due to load imbalance. > > Can someone suggest how I could edit my .mdp file to increase the number of > allowed cells? > -- > 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] periodic-molecules = yes and movie
Dear all, In the simulation of a system in which there is slab, I did not use "periodic-molecules = yes" unfortunately, hence I can not make a good movie out of the trajectory using VMD, the slab move during the movie. The simulation is around 300 ns and I do not want to just waste the CPU time, so, I wonder if there is still any solution for that to make a good movie out of that trajectory? Thank you. Regards, Alex -- 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] Too few cells to run on multiple cores
Hi, I'm having an issue using mdrun in parallel on 48 cores. I'm trying to figure out which options I can include in the .mdp file to increase the number of cells in my system. The full error message is: Initializing Domain Decomposition on 48 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 1.368 nm, LJC Pairs NB, atoms 2123 2152 multi-body bonded interactions: 0.428 nm, Proper Dih., atoms 1105 1113 *Minimum cell size due to bonded interactions: 1.505 nm* Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 0.219 nm Estimated maximum distance required for P-LINCS: 0.219 nm Guess for relative PME load: 0.65 Using 0 separate PME ranks, as guessed by mdrun Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 *Optimizing the DD grid for 48 cells with a minimum initial size of 1.881 nmThe maximum allowed number of cells is: X 3 Y 3 Z 3* --- Program mdrun_mpi, VERSION 5.1 Source code file: /work/y07/y07/gmx/5.1-phase2/source/src/gromacs/domdec/domdec.cpp, line: 6969 Fatal error: There is no domain decomposition for 48 ranks that is compatible with the given box and a minimum cell size of 1.88133 nm I understand the problem -- the system wants to assign one core to each grid cell, but there are only 3x3x3 = 27 cells. I don't know what I can do to fix this problem. The system is a solvated protein bound to a ligand in a ~15 nm box, and it has > 40,000 atoms. I have tried changing the lincs-order and fourier-spacing to no avail. I was able to get the system to run by adding the following flags to mdrun: -rdd 1.2 -dds 0.9 But when I did this, the force imbalance went to > 140%, and 10-30% of the cpu time was lost due to load imbalance. Can someone suggest how I could edit my .mdp file to increase the number of allowed cells? -- 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.
