[gmx-users] decomposition error: -rdd and -dds do not influence the number of ranks

Dear MarK Abraham and Grimaces Users, Due to the limitation of Message body. I would like to open another ticket. I have tried DD control options such as -rdd and -dds but still the same error comes out. The key is to change the number of ranks. These DD control options do not influence the

[gmx-users] Gromacs and Software RDMA over Converged Ethernet -- is there a point ?

Dear Gromacs users: I have access to a new cluster that has GigE interconnect (selected vs. IB for reasons other than cost). As expected, systems that scale nicely to two nodes with IB end up running faster on 1 node than they do in 2 nodes when using GigE. SysAdmins are wondering if software R

Re: [gmx-users] decomposition error

Dear Mark Abraham, I am actually using gromacs with VOTCA Package in order to obtain non-bonded potentials using Iterative Boltzmann inversion (IBI). In the output file, the mdrun would be the following. gmx mdrun -v As I described in the previous email, the error message is related to doma

Re: [gmx-users] decomposition error

Hi, You haven't given us much information about how you're running mdrun, so I can't tell. Much useful material is in the documentation eg. http://manual.gromacs.org/documentation/5.1.3/user-guide/mdrun-performance.html Mark On Sat, 23 Jul 2016 03:34 Chang Woon Jang wrote: > Dear Mark Abraham,

Re: [gmx-users] decomposition error

Dear Mark Abraham, I am a little confused about the number of ranks. How can I choose the number of ranks? Is this mdrun option or something else? Is "number of ranks" different with "number of processors" in parallel machine? Thank you very much for your help. Best regards, Changwoon Jang

Re: [gmx-users] decomposition error

Hi, On Sat, 23 Jul 2016 03:05 Chang Woon Jang wrote: > Dear Mark Abraham, > >Thank you for the details. Do 27, 18, or 12 mean -dds option or > something else? No, the number of ranks. -dds pertains to how much margin DD requires to make sure the largest interactions will be computable over

Re: [gmx-users] decomposition error

Dear Mark Abraham, Thank you for the details. Do 27, 18, or 12 mean -dds option or something else? How can I set up proper DD option? Thank you for your advice. Best regards, Changwoon Jang On Fri, Jul 22, 2016 at 8:58 PM, Mark Abraham wrote: > Hi, > > Well, is it reasonable that your syst

Re: [gmx-users] decomposition error

Hi, Well, is it reasonable that your system has a dihedral where the furthest particles are 1.4nm apart? If so, then your system is quite small with respect to the range of interactions within it, and as that output notes mdrun is limited to three ranks in each direction. So 27, 18 or 12 can give

Re: [gmx-users] decomposition error

Dear Justin Lemkul, I have looked at the log file as below. Initializing Domain Decomposition on 16 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: 0.668 nm, Tab

Re: [gmx-users] decomposition error

On 7/22/16 7:03 PM, Chang Woon Jang wrote: Dear Justin A. Lumkul, Thank you for your answer. I am sorry for asking what is DD. My topology topol.top file is below. Would you please tell me about what is DD? How can I set up in topology file? DD = domain decomposition. Please look in the

Re: [gmx-users] decomposition error

Dear Justin A. Lumkul, Thank you for your answer. I am sorry for asking what is DD. My topology topol.top file is below. Would you please tell me about what is DD? How can I set up in topology file? Thank you. Best regards, Changwoon Jang [ defaults ] ; nbfunccomb-rule gen-p

Re: [gmx-users] decomposition error

On 7/22/16 6:50 PM, Chang Woon Jang wrote: Dear Grimaces Users, I have the decomposition error. I have tried to reduce the number of cores but still have the same problem. In my conf.gro, the cell size is about 5.5x5.5x5.5 but I do not know what the minimum cell size of 1.875nm. Would you pl

[gmx-users] decomposition error

Dear Grimaces Users, I have the decomposition error. I have tried to reduce the number of cores but still have the same problem. In my conf.gro, the cell size is about 5.5x5.5x5.5 but I do not know what the minimum cell size of 1.875nm. Would you please give me some comments or relevant topics a

Re: [gmx-users] load problem

On 7/22/16 4:50 PM, Stephen Chan wrote: Hi Justin, My system has ~55,000 atoms. I tried reducing the number of nodes but the situation didn't improve. I wonder if it's related to plumed performance. That's a rather important detail. Try a vanilla GROMACS run to do benchmarking, then try u

Re: [gmx-users] load problem

Hi Justin, My system has ~55,000 atoms. I tried reducing the number of nodes but the situation didn't improve. I wonder if it's related to plumed performance. Stephen On 07/22/16 22:17, Justin Lemkul wrote: On 7/22/16 3:58 PM, Stephen Chan wrote: Hello all, I'm running an NPT MD on 4 n

[gmx-users] Surface Distribution Function in gromacs

Hi all, A very quick sanity check question regarding one of the gromacs analysis tools. Does the -surf option in gmx_d rdf (or rdf_d in 5.0.#) yield a Surface Distribution Function plot I.e., related to the average density of water molecules around the protein surface? I¹ve tried, and I get a pl

Re: [gmx-users] load problem

On 7/22/16 3:58 PM, Stephen Chan wrote: Hello all, I'm running an NPT MD on 4 nodes and each contains 28 cores. I notice the performance is quite low: vol 0.20! imb F 4% pme/F 0.17 step 7800, remaining wall clock time: 191 s I tried a couple of numbers for -npme (12, 28, 32, 40). None of t

[gmx-users] Amber14sb cutoff

Hi everyone, I would like to use amber14sb forcefield for my RNA-protein complex since it is frequently used in the literature to study RNA-protein complexes. However, I have trouble finding the cut-offs for rlist, rcoulomb, and rvdw (is there any more cutoff I have to change?); I read over this

Re: [gmx-users] topology file format

Table 5.5 of manual, it's the enumerated functional form. On 7/22/2016 1:56 PM, Chang Woon Jang wrote: Dear Grimaces Users, I have a simple question about topology file format. What does "funct" mean in [ bonds ], [ angles ], and [ dihedrals ] terms? Would you please link me where I can

[gmx-users] load problem

Hello all, I'm running an NPT MD on 4 nodes and each contains 28 cores. I notice the performance is quite low: vol 0.20! imb F 4% pme/F 0.17 step 7800, remaining wall clock time: 191 s I tried a couple of numbers for -npme (12, 28, 32, 40). None of these improves the situation. I also ad

[gmx-users] topology file format

Dear Grimaces Users, I have a simple question about topology file format. What does "funct" mean in [ bonds ], [ angles ], and [ dihedrals ] terms? Would you please link me where I can find the topology file format meaning? Thank you. -- Gromacs Users mailing list * Please search the archi

Re: [gmx-users] mdrun -membed Sorry, parallel g_membed is not yet fully functional.

The simulation comes to an end and it produces some output file indeed. Yet, no .gro file is present in the directory. I guess I'm missing something in the process. 2016-07-22 16:54 GMT+02:00 -Mario : > I confirm that it worked smoothly by adding this command. > I think I guessed the role of the

Re: [gmx-users] custom position restraints

Hi, As the warning (and docs) say, position restraint interactions are generated, like other interactions, per molecule(type). You are presumably trying to get them to act on the whole system, which can't be done this way. Mark On Fri, 22 Jul 2016 20:26 Irem Altan wrote: > Hi, > > I am trying

[gmx-users] custom position restraints

Hi, I am trying to override the default position restraints files gromacs creates. However I get the following error during grompp: Fatal error: [ file posre.itp, line 5 ]: Atom index (5) in position_restraints out of bounds (1-2). This probably means that you have inserted topology section "po

Re: [gmx-users] mdrun -membed Sorry, parallel g_membed is not yet fully functional.

On 7/22/16 10:54 AM, -Mario wrote: I confirm that it worked smoothly by adding this command. I think I guessed the role of the command -nt 1, correct me if I'm mistaken: running on single thread avoids parallelization thus it gives no error. Correct. Now another great problem is that in th

Re: [gmx-users] mdrun -membed Sorry, parallel g_membed is not yet fully functional.

I confirm that it worked smoothly by adding this command. I think I guessed the role of the command -nt 1, correct me if I'm mistaken: running on single thread avoids parallelization thus it gives no error. Now another great problem is that in the original study a .gro file is supposed to be produ

Re: [gmx-users] Conversion between nonbonded charmm NBFIX and gromacs cross terms

Thanks. It was actually more to try to see why our simulations have been crashing on NAMD when using Martini, while the systems I built using insane and ran only on gromacs went smoothly. And I still don't know why to be honest, since the simulation (now converted from NAMD to gromacs) actually do

Re: [gmx-users] gmx potential and water

hi Alex, try this paper as a starting point: David van der Spoel and Paul J. van Maaren: The origin of layer structure artifacts in simulation of liquid water J. Chem. Theor. Comp. 2 pp. 1-11 (2006) Andre On Thu, Jul 21, 2016 at 11:07 PM, Alex wrote: > Hi all, > > What we have here is a well-

Re: [gmx-users] angle calculation

Great, thanks a lot! 2016-07-22 15:58 GMT+02:00 Justin Lemkul : > > > On 7/22/16 9:10 AM, Mila Miletić wrote: > >> Hello, >> >> I have recently tried to compute an angle between the COMs of three >> specific groups, >> so what I have done is: >> 1. I used 'gmx gangle' program with a following com

Re: [gmx-users] Conversion between nonbonded charmm NBFIX and gromacs cross terms

As an aside: Martini forcefield parameters are available in Gromacs format on the Martini website. See http://cgmartini.nl/index.php/force-field-parameters Peter On Thu, Jul 21, 2016 at 2:05 PM, Marlon Sidore wrote: > Thanks for your answer, that solved everything. > > Marlon > > Marlon Sidore

Re: [gmx-users] Problem with Umbrella Sampling simulation

Dear Justin I am really grateful for your help. I have based my job on your tutorial, but I had to adapt it to my case study . I also use a different version of gromacs. I used .mdp your files as templates, but I have adapted to my problem. Thanks for your help Best regards, D.V. 2016-07-22

Re: [gmx-users] angle calculation

On 7/22/16 9:10 AM, Mila Miletić wrote: Hello, I have recently tried to compute an angle between the COMs of three specific groups, so what I have done is: 1. I used 'gmx gangle' program with a following command: gmx gangle -f *.xtc -s *.tpr -n index.ndx -g1 vector -group1 "com of group "g1"

Re: [gmx-users] Problem with Umbrella Sampling simulation

On 7/22/16 9:13 AM, Daniele Veclani wrote: Dear Justin Thank you for your answer. So I use this .mdp file for fast NPT equilibration: ; Run control integrator = sd ; Langevin dynamics dt = 0.002 nsteps = 5; 0.1 ns nstcomm

Re: [gmx-users] Reference file for harmonic restraints

On 7/22/16 9:53 AM, CROUZY Serge 119222 wrote: Hi all, I'm running several sequential minimizations and MD simulations with gromacs after translation of part of my system (the rest being harmonically restrained) and I'm looking for a way to specify unique reference coordinates for all simul

[gmx-users] Reference file for harmonic restraints

Hi all, I'm running several sequential minimizations and MD simulations with gromacs after translation of part of my system (the rest being harmonically restrained) and I'm looking for a way to specify unique reference coordinates for all simulations The way I understand Gromacs, you define a p

Re: [gmx-users] Problem with Umbrella Sampling simulation

Dear Justin Thank you for your answer. So I use this .mdp file for fast NPT equilibration: ; Run control integrator = sd ; Langevin dynamics dt = 0.002 nsteps = 5; 0.1 ns nstcomm = 10 ; Output control nstxout

Re: [gmx-users] angle calculation

Hello, I have recently tried to compute an angle between the COMs of three specific groups, so what I have done is: 1. I used 'gmx gangle' program with a following command: gmx gangle -f *.xtc -s *.tpr -n index.ndx -g1 vector -group1 "com of group "g1" plus com of group "g2"" -g2 vector -group2 "

Re: [gmx-users] Problem with Umbrella Sampling simulation

On 7/22/16 8:19 AM, Daniele Veclani wrote: Dear Gromacs Users I'm trying to calculate the potential mean force between two molecules (A and B). I created the various configurations through the pull simulation. To do this I kept fixes the position of the molecule A (position restraint) I have

[gmx-users] Problem with Umbrella Sampling simulation

Dear Gromacs Users I'm trying to calculate the potential mean force between two molecules (A and B). I created the various configurations through the pull simulation. To do this I kept fixes the position of the molecule A (position restraint) I have extracted the coordinates and sampled the vari

Re: [gmx-users] SHAKE error

Yes this could be the reason. Thanks Justin. > On 22 Jul 2016, at 14:00, Justin Lemkul wrote: > > > > On 7/22/16 7:59 AM, gozde ergin wrote: >> No I am using same Gromacs 4.6.5. >> I run these two simulations again one runs and the other fails with the same >> .mdp file. >> > > Since the err

Re: [gmx-users] SHAKE error

On 7/22/16 7:59 AM, gozde ergin wrote: No I am using same Gromacs 4.6.5. I run these two simulations again one runs and the other fails with the same .mdp file. Since the error is DD-specific, probably your earlier run did not include the same exact setup, either in terms of number of proc

Re: [gmx-users] SHAKE error

No I am using same Gromacs 4.6.5. I run these two simulations again one runs and the other fails with the same .mdp file. > On 22 Jul 2016, at 13:53, Justin Lemkul wrote: > > > > On 7/22/16 7:50 AM, gozde ergin wrote: >> Dear all, >> >> I use md-vv and SHAKE algorithm however I face an erro

Re: [gmx-users] SHAKE error

On 7/22/16 7:50 AM, gozde ergin wrote: Dear all, I use md-vv and SHAKE algorithm however I face an error which I was not before. Before I had 1-decanol and water system and now I have cis-pionic and water system. I exactly use the same .mdp file just as before however this error comes : SHAK

Re: [gmx-users] DT Fatal Error still remaining

On 7/22/16 7:49 AM, Sanjay Singh wrote: I encountered a problem when I using pdb2gmx to convert a pdb file into gro and top file.by using 6: AMBER99SB-ILDN protein, nucleic AMBER94 Force field The system give me a fatal error message as following:Atom P in residue DT 501 was not found in rtp

[gmx-users] SHAKE error

Dear all, I use md-vv and SHAKE algorithm however I face an error which I was not before. Before I had 1-decanol and water system and now I have cis-pionic and water system. I exactly use the same .mdp file just as before however this error comes : SHAKE is not supported with domain decomposit

[gmx-users] DT Fatal Error still remaining

I encountered a problem when I using pdb2gmx to convert a pdb file into gro and top file.by using 6: AMBER99SB-ILDN protein, nucleic AMBER94 Force field The system give me a fatal error message as following:Atom P in residue DT 501 was not found in rtp entry DT5 with 30 atoms while sorting atoms.

Re: [gmx-users] PSCP

See http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00397 for an example of a PSCP in GROMACS (although it was from crystal to crystal). It takes series of different .mdps to do it. On Fri, Jul 22, 2016 at 5:34 AM, Justin Lemkul wrote: > > > On 7/21/16 11:20 PM, kar...@shell.com wrote: >> >> Hell

Re: [gmx-users] Analyzing trajectory file always stops.

On 7/21/16 9:19 PM, yamashita.ryoto@st.kyoto-u.ac.jp wrote: Dear all. I have a trouble when analyzing my trajectory file. I want to calculate the radius of gyration of oligomer.But when calculating the radius of gyration, the calculations always stop at about two thirds of my trajectory f

Re: [gmx-users] PSCP

On 7/21/16 11:20 PM, kar...@shell.com wrote: Hello Justin! In recent literature, a pseudo-supercritical path has been used to model the melting point of crystals. To do so, the molecule starts in the liquid state, (1) has the intermolecular forces scaled down (which I did using lambda and f

Re: [gmx-users] visualization of output of GridMAT-Md results

On 7/22/16 1:20 AM, kamakshi sikka wrote: Hello all, I am trying to calculate the area per lipid and thickness of membrane with peptide using *GridMAT-MD 2.0*. However, I don’t know how to visualize the output files (like output.frame1.20x20.bottom_areas.dat). There's nothing to visualize.

Re: [gmx-users] Help with installation of gromacs

use source /usr/local/gromacs/bin/GMXRC before executing pdb2gmx On Thu, Jul 21, 2016 at 12:36 PM, Sidra Rafi wrote: > Dear Omamuyovwi, > > You have to define your path variable. you can use bash for this purpose. > then it will work. > > > > On Wed, Jul 20, 2016 at 8:49 PM, Omamuyovwi Akemu <