[gmx-users] Re: pull=constraint gives zero forces
alex.bjorling
alex.bjorling at gmail.com
Tue Oct 9 12:09:25 CEST 2012
Hi Erik,
Yes - I had a feeling I'd read that in the manual somewhere, which was
why I tried replacing such constraints with bonds. As I wrote above,
the LINCS warnings disappeared but the segfault remained.
Alex
2012/10/9 Erik Marklund [via GROMACS] <ml-node+s5086n5001821h19 at n6.nabble.com>:
> 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]
>>> <
>>
>>> 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
>>>>> 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
>
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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
> [hidden email]
> http://www2.icm.uu.se/molbio/elflab/index.html
>
>
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