Re: [gmx-users] Using Gpus on multiple nodes. (Feature #1591)
Try: mpirun -npernode 2 -Trayder On Wed, Oct 15, 2014 at 8:42 AM, Siva Dasetty wrote: > Thank you Mark for the reply, > > We use pbs for submitting jobs on our cluster and this is how I request the > nodes and processors > > #PBS -l > select=2:ncpus=8:mem=8gb:mpiprocs=8:ngpus=2:gpu_model=k20:interconnect=fdr > > > Do you think the problem could be with the way I installed mdrun using Open > MPI? > > > Can you please suggest the missing environmental settings that I may need > to include in the job script in order for the MPI to consider 2 ranks on > one node? > > > Thank you for your time. > > > > On Tue, Oct 14, 2014 at 5:20 PM, Mark Abraham > wrote: > > > On Tue, Oct 14, 2014 at 10:51 PM, Siva Dasetty > > wrote: > > > > > Dear All, > > > > > > I am currently able to run simulation on a single node containing 2 > gpus, > > > but I get the following fatal error when I try to run the simulation > > using > > > multiple gpus (2 on each node) on multiple nodes (2 for example) using > > OPEN > > > MPI. > > > > > > > Here you say you want 2 ranks on each of two nodes... > > > > > > > Fatal error: > > > > > > Incorrect launch configuration: mismatching number of PP MPI processes > > and > > > GPUs > > > > > > per node. > > > > > > mdrun was started with 4 PP MPI processes per node, > > > > > > ... but here mdrun means what it says... > > > > > > > but you provided only 2 > > > GPUs. > > > > > > The command I used to run the simulation is > > > > > > mpirun -np 4 mdrun -s -deffnm <...> -gpu_id 01 > > > > > > > ... which means your MPI environment (hostfile, job script settings, > > whatever) doesn't have the settings you think it does, since it's putting > > all 4 ranks on one node. > > > > Mark > > > > > > > > > > > > > However It at least runs if I use the following command, > > > > > > > > > mpirun -np 4 mdrun -s -deffnm <...> -gpu_id 0011 > > > > > > > > > But after referring to the following thread, I highly doubt if I am > using > > > all the 4 gpus available in the 2 nodes combined. > > > > > > > > > > > > > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-May/007682.html > > > > > > > > > > > > Thank you for your help in advance, > > > > > > -- > > > Siva > > > -- > > > 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. > > > > > > -- > Siva > -- > 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] (no subject)
Hello, I am doing Molecular-Dynamic simulation of Protein-Ligand complex embedded in POPC lipid membrane. After energy minimizing of complex, I am facing problem with NVT equilibration step. mdrun crashed with following error: "12 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated." These are the parameters used in nvt.mdp file: title = NVT equilibration define = -DPOSRES_LIPID -DPOSRES -DPOSRES_WATER ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_LMT POPC Water_and_ions ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 271 271 271 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 271 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_LMT_POPC Water_and_ions Please help me... -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin 176206, District Kangra,* *Himachal Pradesh, India* -- 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] 2-D liquid
Hi users, I am trying to simulate 2-d liquids interacting with simple potential like Lennard-Jones potential. Can it be done by specifying "pcoupletype = semiisotropic" in the .mdp file? I mean enforcing a normal pressure in x-y direction while very high pressure in z direction to constrain the motion in z. Or do I need to define walls in the z direction? Does anyone have similar experience? Your help are highly appreciated! Cai -- 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] How long run should be enough for Free Energy Calculation of a protein?
Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? Batsaikhan -- 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] Using Gpus on multiple nodes. (Feature #1591)
Thank you Mark for the reply, We use pbs for submitting jobs on our cluster and this is how I request the nodes and processors #PBS -l select=2:ncpus=8:mem=8gb:mpiprocs=8:ngpus=2:gpu_model=k20:interconnect=fdr Do you think the problem could be with the way I installed mdrun using Open MPI? Can you please suggest the missing environmental settings that I may need to include in the job script in order for the MPI to consider 2 ranks on one node? Thank you for your time. On Tue, Oct 14, 2014 at 5:20 PM, Mark Abraham wrote: > On Tue, Oct 14, 2014 at 10:51 PM, Siva Dasetty > wrote: > > > Dear All, > > > > I am currently able to run simulation on a single node containing 2 gpus, > > but I get the following fatal error when I try to run the simulation > using > > multiple gpus (2 on each node) on multiple nodes (2 for example) using > OPEN > > MPI. > > > > Here you say you want 2 ranks on each of two nodes... > > > > Fatal error: > > > > Incorrect launch configuration: mismatching number of PP MPI processes > and > > GPUs > > > > per node. > > > > mdrun was started with 4 PP MPI processes per node, > > > ... but here mdrun means what it says... > > > > but you provided only 2 > > GPUs. > > > > The command I used to run the simulation is > > > > mpirun -np 4 mdrun -s -deffnm <...> -gpu_id 01 > > > > ... which means your MPI environment (hostfile, job script settings, > whatever) doesn't have the settings you think it does, since it's putting > all 4 ranks on one node. > > Mark > > > > > > > > However It at least runs if I use the following command, > > > > > > mpirun -np 4 mdrun -s -deffnm <...> -gpu_id 0011 > > > > > > But after referring to the following thread, I highly doubt if I am using > > all the 4 gpus available in the 2 nodes combined. > > > > > > > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-May/007682.html > > > > > > > > Thank you for your help in advance, > > > > -- > > Siva > > -- > > 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. > -- Siva -- 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] Using Gpus on multiple nodes. (Feature #1591)
On Tue, Oct 14, 2014 at 10:51 PM, Siva Dasetty wrote: > Dear All, > > I am currently able to run simulation on a single node containing 2 gpus, > but I get the following fatal error when I try to run the simulation using > multiple gpus (2 on each node) on multiple nodes (2 for example) using OPEN > MPI. > Here you say you want 2 ranks on each of two nodes... > Fatal error: > > Incorrect launch configuration: mismatching number of PP MPI processes and > GPUs > > per node. > > mdrun was started with 4 PP MPI processes per node, ... but here mdrun means what it says... > but you provided only 2 > GPUs. > > The command I used to run the simulation is > > mpirun -np 4 mdrun -s -deffnm <...> -gpu_id 01 > ... which means your MPI environment (hostfile, job script settings, whatever) doesn't have the settings you think it does, since it's putting all 4 ranks on one node. Mark > > > However It at least runs if I use the following command, > > > mpirun -np 4 mdrun -s -deffnm <...> -gpu_id 0011 > > > But after referring to the following thread, I highly doubt if I am using > all the 4 gpus available in the 2 nodes combined. > > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-May/007682.html > > > > Thank you for your help in advance, > > -- > Siva > -- > 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] Using Gpus on multiple nodes. (Feature #1591)
Dear All, I am currently able to run simulation on a single node containing 2 gpus, but I get the following fatal error when I try to run the simulation using multiple gpus (2 on each node) on multiple nodes (2 for example) using OPEN MPI. Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun was started with 4 PP MPI processes per node, but you provided only 2 GPUs. The command I used to run the simulation is mpirun -np 4 mdrun -s -deffnm <...> -gpu_id 01 However It at least runs if I use the following command, mpirun -np 4 mdrun -s -deffnm <...> -gpu_id 0011 But after referring to the following thread, I highly doubt if I am using all the 4 gpus available in the 2 nodes combined. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-May/007682.html Thank you for your help in advance, -- Siva -- 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] Conserved energy ("Conserved En.") in NVT simulation
Dear Mark and ALL, I am trying to calculate the conserved energy (H-tilde) in Bussi's stochastic velocity rescale algorithm (jcp,2007). In previous maillist, Mark had mentioned that the conserved En. in ener file is the H in bussi's paper (http://permalink.gmane.org/gmane.science.biology.gromacs.user/63005). According to the eq. 15 in Bussi's paper, we just need to get the time integration of dK if we have had the H. I carefully checked the coupling.c file, and noticed a variable - therm_integral[i] in the fucntion vrescale_tcoupl(). The therm_integral[i]-= Ek_new - Ek. It seems like an accumulation of the -dK. If it realy is the sum of -dK, the problem could become simple. What we need to do is just like this: H-tilde=H-Tau-t* therm_integral[i].? Is that right? I really need your help. Any suggestion is valuable. Wade -- 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] grompp Segmentation fault
Here are more details .itp file ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_991 Cu2963.546001.098 A3.114e-010.02092e+00 opls_993 OA8 15.99940-0.665 A3.033e-01 0.401664e+00 opls_994 OB8 15.99940-0.665 A3.033e-01 0.401664e+00 opls_995 CA6 12.0110 0.778 A3.473e-01 0.39748e+00 opls_996 CB6 12.0110 -0.092 A3.473e-01 0.39748e+00 opls_997 CC6 12.0110 -0.014 A3.473e-01 0.39748e+00 opls_998 HM1 1.0080 0.109 A2.846e-01 0.06276e+00 [ bondtypes ] ; ij func b0D Beta Cu OA 3 0.1969 358.8574960.285 Cu OB 3 0.1969 358.8574960.285 OA CA 3 0.1260 564.840.200 OB CA 3 0.1260 564.840.200 CA CB 3 0.1456 367.52256 0.200 CB CC 3 0.1355 502.080.200 CC HM 3 0.0931 485.344 0.177 [ angletypes ] ; ijk func th0 cth OA Cu OA 1 170.2 419.73888 OB Cu OB 1 170.2 419.73888 OA Cu OB 190.0 100.416 Cu OA CA 1 127.5 338.65296 Cu OB CA 1 127.5 338.65296 OA CA OA 1 128.5 606.68 OB CA OB 1 128.5 606.68 OA CA OB 1 128.5 606.68 OA CA CB 1 116.2 456.01416 OB CA CB 1 116.2 456.01416 CA CB CC 1 119.9 290.20224 CC CB CC 1 120.1 753.12 CB CC CB 1 119.9 753.12 CB CC HM 1 120.0 309.616 [ dihedraltypes ] ; ijkl func coefficients ; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form ; according to the formula in the Gromacs manual. CuOA CA CB1 180.012.552 2 CuOB CA CB1 180.012.552 2 CuOA CA OB1 180.012.552 2 CuOB CA OA1 180.012.552 2 CuOA CA OA1 180.012.552 2 CuOB CA OB1 180.012.552 2 CBCC CB CC1 180.012.552 2 CACB CC CB1 180.012.552 2 CACB CC HM1 180.012.552 2 CCCB CC HM1 180.012.552 2 OACA CB CC1 180.010.460 2 OBCA CB CC1 180.010.460 2 HMCC CB CB2 180.01.548082 CACB CC CC2 180.0 41.84 2 CBCA OA OB2 180.0 41.84 2 CBCA OB OA2 180.0 41.84 2 Initial part of .gro file Title 156 1BTC OA1 1 19.579 14.561 18.006 0. 0. 0. 1BTC CA2 2 18.533 15.007 18.533 0. 0. 0. 1BTC CB3 3 17.865 16.163 17.865 0. 0. 0. 1BTC CC4 4 18.433 16.737 16.737 0. 0. 0. 1BTC HM5 5 19.215 16.358 16.358 0. 0. 0. 1BTC CC6 6 16.737 16.737 18.433 0. 0. 0. 1BTC HM7 7 16.358 16.358 19.215 0. 0. 0. 1BTC OA8 8 14.561 18.006 19.579 0. 0. 0. 1BTC CA9 9 15.007 18.533 18.533 0. 0. 0. 1BTC CB1010 16.163 17.865 17.865 0. 0. 0. 1BTC CC1111 16.737 18.433 16.737 0. 0. 0. 1BTC HM1212 16.358 19.215 16.358 0. 0. 0. 1BTC OA1313 18.006 19.579 14.561 0. 0. 0. 1BTC CA1414 18.533 18.533 15.007 0. 0. 0. 1BTC CB1515 17.865 17.865 16.163 0. 0. 0. 1BTC OB1616 14.561 19.579 18.006 0. 0. 0. 1BTC OB1717 18.006 14.561 19.579 0. 0. 0. 1BTC OB1818 19.579 18.006 14.561 0. 0. 0. 1BTC OA1919 14.561 21.499 19.926 0. 0. 0. 1BTC CA2020 15.007 20.972 20.972 0. 0. 0. 1BTC CB2121 16.163 21.639 21.639 0. 0. 0. 1BTC CC2222 16.737 22.767 21.072 0. 0. 0. 1BTC HM2323 16.358 23.146 20.290 0. 0. 0. 1BTC CC2424 16.737 21.072 22.767 0. 0. 0. 1BTC HM2525 16.358 20.290 23.146 0. 0. 0. 1BTC OB2626 14.561 19.926 21.499 0. 0. 0. 1BTC OA2727 19.926 14.561 21.499 0. 0. 0. 1BTC CA2828 20.
Re: [gmx-users] Problem with constraints in NVT calculations.
On 10/14/14 7:40 AM, Kester Wong wrote: Hi Justin and all, > > > > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > > > example I came across is from the work by Ho and Striolo > > > > > > titled: Polarizability effects in molecular dynamics simulations of the > > > graphene-water interface > > > > > > > Of course you can implement whatever you like. Gromacs has been able to carry > > out polarizable simulations for a very long time; I've only ever cautioned > > against abuse of certain models. > > > > > > I guess that GROMACS is capable in running polarisable sims, but for the Drude > > polarisable calcs, they are prone to polarisation catastrophe due to the > > massless shells and thermostat instability? > > Polarization catastrophe is possible in any polarizable simulation. Usually > very small time steps are required to avoid this, unless using an anharmonic > potential or a hard wall restraint. > > > Using Morse = yes for the anharmonic potential option, whereas using the > parameters below for the hard wall restraint option? > > pbc = xy > nwall = 2 > wall-atomtype =; optional > wall-type = 12-6 > wall-r-linpot = 1 ; having a positive val. is esp. useful in equil. run > wall-density = 5 5 > wall-ewald-zfac = 3 > No. I'm not suggesting a Morse potential. What I was referring to was an anharmonic function for the bonds, which is present in Gromacs but I'm not sure if it's documented. The wall settings in Gromacs have nothing to do with this. Such a function is not present in Gromacs (yet). Although the wall settings have nothing to do with polarisation catastrophe, I guess it might be useful in the following case: I have been using a time step of 1 fs, which is small already, yet the water droplet (on graphene) quickly fills up the vacuum of ~5-6 nm along the z-direction. I will try using the wall setup as above, hoping that water remains a droplet with the presence of H3O and Cl ions. Could you please explain what is the difference between the three types of wall; 9-3, 10-4, and 12-6? The exponents used in the LJ potential for the wall. 12-6 is the "normal" LJ potential. The only part of the GROMACS 5.0 manual that described anharmonic bond potential is in the Morse potential section 4.2.2. Like I said, it's not documented. See src/gromacs/gmxlib.c, function anharm_polarize(). Which function is not available in GROMACS yet? What we call the "hard wall" restraint, that reflects a Drude particle along the bond vector connecting it to its parent atom. It prevents the Drude from moving more than a specified amount, thus vastly improving integration stability. See the Appendix of dx.doi.org/10.1021/jp402860e. > > In the paper mentioned above, the authors have carried out three types of cals: > > i) SPC/E on non-pol graphene > > ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states > > iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite > > charge): graphene-DP in neutral or charged states > > > > They seemed to have simulated their systems using both additive and polarisable > > (0.878 angstrom^3) models? > > I guess this is where I got confused. > > I suppose you can make any model work if you parametrize it a certain way, but > my point in the previous message is that you shouldn't go off trying to build a > force field that has SWM4-NDP water around additive CHARMM solutes. > > > Yep, now I understand it. > If I wanted to also describe graphene, is it possible to include carbon > parameters in the SWM4-NDP force field then? > Well, strictly speaking, you're not introducing graphene into a SWM4-NDP force field, you're creating a force field that describes both. This can certainly be done if you have all the parameters. That is great! To create a FF that describes the SWM4 water, NDP ions, and graphene carbon (CA); I will have to include graphene.itp, the CA-CA bonded parameters, and the LJ nonbonding interaction parameters, is that right? Yes. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailin
Re: [gmx-users] regarding confout.gro
On 10/14/14 12:31 AM, RINU KHATTRI wrote: hello gromacs user i am working on protein ligand complex with popc membrane i am running production md in extended time (40 ns) i got some file i am using -noappend option i got confout.gro file in each extended time what is the use of this file if i want see my protein or ligand are in proper place this confout.gro is sufficient of i have to see traj file The confout.gro file is simply the last snapshot of the simulation interval. Whether or not it is reflective of the dynamics during that interval is unknown without doing analysis and simple visualization. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] grompp Segmentation fault
On 10/13/14 10:42 PM, Nilesh Dhumal wrote: hello, I running grompp for simulation. I get Segmentation fault error. grompp -f 600.mdp -c cu.gro -p cu_btc_1.top -o 1.tpr checking input for internal consistency... processing topology... Segmentation fault Could any one tell what is the problem? Not without a full debugging back trace. Seg faults are generic memory errors; there's nothing at all that can be diagnosed from this message alone. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Problem with constraints in NVT calculations.
Hi Justin and all,> > > > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > > > example I came across is from the work by Ho and Striolo > > > > > > titled: Polarizability effects in molecular dynamics simulations of the > > > graphene-water interface > > > > > > > Of course you can implement whatever you like. Gromacs has been able to carry > > out polarizable simulations for a very long time; I've only ever cautioned > > against abuse of certain models. > > > > > > I guess that GROMACS is capable in running polarisable sims, but for the Drude > > polarisable calcs, they are prone to polarisation catastrophe due to the > > massless shells and thermostat instability? > > Polarization catastrophe is possible in any polarizable simulation. Usually > very small time steps are required to avoid this, unless using an anharmonic > potential or a hard wall restraint. > > > Using Morse = yes for the anharmonic potential option, whereas using the > parameters below for the hard wall restraint option? > > pbc = xy > nwall = 2 > wall-atomtype =; optional > wall-type = 12-6 > wall-r-linpot = 1 ; having a positive val. is esp. useful in equil. run > wall-density = 5 5 > wall-ewald-zfac = 3 > No. I'm not suggesting a Morse potential. What I was referring to was an anharmonic function for the bonds, which is present in Gromacs but I'm not sure if it's documented. The wall settings in Gromacs have nothing to do with this. Such a function is not present in Gromacs (yet). Although the wall settings have nothing to do with polarisation catastrophe, I guess it might be useful in the following case: I have been using a time step of 1 fs, which is small already, yet the water droplet (on graphene) quickly fills up the vacuum of ~5-6 nm along the z-direction. I will try using the wall setup as above, hoping that water remains a droplet with the presence of H3O and Cl ions. Could you please explain what is the difference between the three types of wall; 9-3, 10-4, and 12-6?The only part of the GROMACS 5.0 manual that described anharmonic bond potential is in the Morse potential section 4.2.2.Which function is not available in GROMACS yet?> > In the paper mentioned above, the authors have carried out three types of cals: > > i) SPC/E on non-pol graphene > > ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states > > iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite > > charge): graphene-DP in neutral or charged states > > > > They seemed to have simulated their systems using both additive and polarisable > > (0.878 angstrom^3) models? > > I guess this is where I got confused. > > I suppose you can make any model work if you parametrize it a certain way, but > my point in the previous message is that you shouldn't go off trying to build a > force field that has SWM4-NDP water around additive CHARMM solutes. > > > Yep, now I understand it. > If I wanted to also describe graphene, is it possible to include carbon > parameters in the SWM4-NDP force field then? > Well, strictly speaking, you're not introducing graphene into a SWM4-NDP force field, you're creating a force field that describes both. This can certainly be done if you have all the parameters. That is great! To create a FF that describes the SWM4 water, NDP ions, and graphene carbon (CA); I will have to include graphene.itp, the CA-CA bonded parameters, and the LJ nonbonding interaction parameters, is that right? > > > > On the side: From my previous calcs using GRAPPA force field (TIPS3P water > > model), graphene's polarisation (0.91 angstrom^3) resulted in spreading of water > > into thin layer. But that was polarisable graphene in a rigid rod model (dummy > > instead of shelltype particle). > > > > > > > > Pardon me if this sounds outright wrong; regarding the massless Drude particle, > > > can it be replaced with an atom (assuming an induced dipole model) instead of > > > the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an > > > opposite charge of the water oxygen atom? > > > > > > > In the Drude model with 0.4-amu particles, the Drudes are essentially just > > atoms. There's nothing conceptually special about them, we just handle them > > slightly differently in the code. > > > > > > Well since domain decomposition will not work on shelltype calcs, I am intrigued > > to experiment if I can: > > i) replace the Drudes to atom with the same configuration - opposite charge, > > mass (0.4 amu), lengths, etc > > > > The problem is that shells/Drudes have to be relaxed (SCF) or otherwise h
[gmx-users] Free energy calculation of
Dear gxm users,
Now I am doing solvation free energy of a protein, I follow Sander Pronk's
tutorial downloaded from Gromacs page.
1. How do I check system is equilibrated?
2. I run following command
sh mklambdas.sh run.mdp topol.top equil.gro
I got following error:
mklambdas.sh: 12: mklambdas.sh: Syntax error: "(" unexpected
How can I fix this?
Best regards,
Batsaikhan
--
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.
