Hi, Do you know there are issues with using pull=constraint on molecules that have constrained bonds? It's mentioned in the manual somewhere.
Erik 9 okt 2012 kl. 11.39 skrev alex.bjorling: > Sorry - forgot to mention that before crashing, the run with all other > constraints removed produces a single line of pullf output: > > 0.0000 -812.401 -4002.84 482.04 1951.47 138.953 -1806.55 > > -601.007 2644.79 447.018 1768.6 -214.64 -199.829 -2746.97 > > 1177.7 476.39 288.535 -559.274 123.08 114.493 851.86 550.558 > > As Thomas Schlesier mentions here, > http://gromacs.5086.n6.nabble.com/pull-constraint-gives-zero-forces-tp5001817.html, > the pullf output apparently contains the forces necessary to enforce the > constraints. > > / Alex > > > alex.bjorling wrote >> Thanks guys, >> >> Fixing the bug, recompiling and trying again results in a segfault >> like with version 4.0.7. I interpret this as GROMACS working fine, and >> suppose that there's something wrong with my input. Will continue this >> thread here and would really appreciate any ideas on how to proceed. >> >> Before the segfault, I get a bunch of LINCS warnings, all concerning >> atoms that have other constraints in the topology. Manually replacing >> these by stiff bonds in the itp gets rid of the LINCS warnings, but >> still produces an immediate segfault. >> >> The complete mdp follows. (Chris: previously posted via the web forum >> - it seems then you have to click the nabble link to see it). >> >> Cheers, >> Alex >> >> 50_constr3.mdp: >> ****************************************************************** >> pull = constraint >> pull_geometry = position >> pull_dim = Y Y Y >> pull_start = yes >> pull_group0 = BB >> pull_nstxout = 1000 >> pull_nstfout = 1000 >> pull_ngroups = 7 >> pull_constr_tol = 1e-6 >> >> pull_group1 = group1 >> pull_init1 = 0.0 0.0 0.0 >> pull_rate1 = 0.0 0.0 0.0 >> >> pull_group2 = group2 >> pull_init2 = 0.0 0.0 0.0 >> pull_rate2 = 0.0 0.0 0.0 >> >> pull_group3 = group3 >> pull_init3 = 0.0 0.0 0.0 >> pull_rate3 = 0.0 0.0 0.0 >> >> pull_group4 = group4 >> pull_init4 = 0.0 0.0 0.0 >> pull_rate4 = 0.0 0.0 0.0 >> >> pull_group5 = group5 >> pull_init5 = 0.0 0.0 0.0 >> pull_rate5 = 0.0 0.0 0.0 >> >> pull_group6 = group6 >> pull_init6 = 0.0 0.0 0.0 >> pull_rate6 = 0.0 0.0 0.0 >> >> pull_group7 = group7 >> pull_init7 = 0.0 0.0 0.0 >> pull_rate7 = 0.0 0.0 0.0 >> >> ; >> ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 or 2.1 >> ; >> >> ; TIMESTEP IN MARTINI >> ; Most simulations are numerically stable >> ; with dt=40 fs, some (especially rings) require 20-30 fs. >> ; Note that time steps of 40 fs and larger may create local heating or >> ; cooling in your system. Although the use of a heat bath will globally >> ; remove this effect, it is advised to check consistency of >> ; your results for somewhat smaller time steps in the range 20-30 fs. >> ; Time steps exceeding 40 fs should not be used; time steps smaller >> ; than 20 fs are also not required. >> >> ;define = -DPOSRES >> integrator = md >> tinit = 0.0 >> dt = 0.02 >> nsteps = 2500000 ; 50 ns >> nstcomm = 1 >> comm-grps = >> >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstenergy = 100 >> nstxtcout = 1000 >> xtc_precision = 100 >> xtc-grps = >> energygrps = Protein >> >> ; NEIGHBOURLIST and MARTINI >> ; Due to the use of shifted potentials, the noise generated >> ; from particles leaving/entering the neighbour list is not so large, >> ; even when large time steps are being used. In practice, once every >> ; ten steps works fine with a neighborlist cutoff that is equal to the >> ; non-bonded cutoff (1.2 nm). However, to improve energy conservation >> ; or to avoid local heating/cooling, you may increase the update frequency >> ; and/or enlarge the neighbourlist cut-off (to 1.4 nm). The latter option >> ; is computationally less expensive and leads to improved energy >> conservation >> >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> rlist = 1.4 >> >> ; MARTINI and NONBONDED >> ; Standard cut-off schemes are used for the non-bonded interactions >> ; in the Martini model: LJ interactions are shifted to zero in the >> ; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2 >> nm. >> ; The treatment of the non-bonded cut-offs is considered to be part of >> ; the force field parameterization, so we recommend not to touch these >> ; values as they will alter the overall balance of the force field. >> ; In principle you can include long range electrostatics through the use >> ; of PME, which could be more realistic in certain applications >> ; Please realize that electrostatic interactions in the Martini model are >> ; not considered to be very accurate to begin with, especially as the >> ; screening in the system is set to be uniform across the system with >> ; a screening constant of 15. When using PME, please make sure your >> ; system properties are still reasonable. >> >> coulombtype = Shift >> rcoulomb_switch = 0.0 >> rcoulomb = 1.2 >> epsilon_r = 15 >> vdw_type = Shift >> rvdw_switch = 0.9 >> rvdw = 1.2 >> DispCorr = No >> >> ; MARTINI and TEMPRATURE/PRESSURE >> ; normal temperature and pressure coupling schemes can be used. >> ; It is recommended to couple individual groups in your system separately. >> ; Good temperature control can be achieved with the Berendsen thermostat, >> ; using a coupling constant of the order of Ï„ = 1 ps. Even better >> ; temperature control can be achieved by reducing the temperature coupling >> ; constant to 0.1 ps, although with such tight coupling (Ï„ approaching >> ; the time step) one can no longer speak of a weak-coupling scheme. >> ; We therefore recommend a coupling time constant of at least 0.5 ps. >> ; >> ; Similarly, pressure can be controlled with the Berendsen barostat, >> ; with a coupling constant in the range 1-5 ps and typical compressibility >> ; in the order of 10-4 - 10-5 bar-1. Note that, in order to estimate >> ; compressibilities from CG simulations, you should use Parrinello-Rahman >> ; type coupling. >> >> tcoupl = Berendsen >> tc-grps = system >> tau_t = 1.0 >> ref_t = 320 >> Pcoupl = berendsen >> Pcoupltype = isotropic >> tau_p = 2.0 >> compressibility = 3e-4 >> ref_p = 1.0 >> >> gen_vel = no >> gen_temp = 320 >> gen_seed = 473529 >> >> ; MARTINI and CONSTRAINTS >> ; for ring systems constraints are defined >> ; which are best handled using Lincs. >> ; Note, during energy minimization the constrainst should be >> ; replaced by stiff bonds. >> >> constraints = none >> constraint_algorithm = Lincs >> unconstrained_start = no >> lincs_order = 4 >> lincs_warnangle = 30 >> >> ****************************************************************** >> >> >> >> 2012/10/9 Jaakko Uusitalo [via GROMACS] >> < > >> [email protected] > >> >: >>> >>> constraint pulling has a bug in 4.5.5, see: >>> http://redmine.gromacs.org/issues/825. I'm guessing that's causing your >>> problems. Fixing it is very easy (see the link) or you can also use an >>> earlier version like 4.5.3 that works. >>> >>> On 9.10.12 2:26 , Christopher Neale wrote: >>> >>>> Please post your entire .mdp file and a snip of the output in your pullf >>>> and pullc files. >>>> (Your initial post on this topic was also missing these, although the >>>> text >>>> reads as if you intended to include them). >>>> >>>> Chris. >>>> >>>> -- original message -- >>>> >>>> Following up on this post. I've tried the same runs using version 4.0.7, >>>> which gave immediate segmentation faults. Not sure if this is a clue or >>>> a >>>> trivial consequence of switching versions, but there it is. >>>> >>>> Any other ideas why the pullf output just contains zeros? >>>> >>>> Cheers, >>>> Alex > > > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/pull-constraint-gives-zero-forces-tp5001538p5001819.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
