[gmx-users] Re: pull=constraint gives zero forces
erikm at xray.bmc.uu.se
Tue Oct 9 11:53:42 CEST 2012
Do you know there are issues with using pull=constraint on molecules that have constrained bonds? It's mentioned in the manual somewhere.
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,
> the pullf output apparently contains the forces necessary to enforce the
> / 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).
>> 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
>> 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
>> ; 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]
>> ml-node+s5086n5001810h78 at .nabble
>>> 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
>>>> reads as if you intended to include them).
>>>> -- 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
>>>> trivial consequence of switching versions, but there it is.
>>>> Any other ideas why the pullf output just contains zeros?
> 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.
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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
erikm at xray.bmc.uu.se
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