[gmx-users] Re: pull=constraint gives zero forces
alex.bjorling
alex.bjorling at gmail.com
Tue Oct 9 10:40:18 CEST 2012
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 n6.nabble.com>:
>
> 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-tp5001538p5001814.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
More information about the gromacs.org_gmx-users
mailing list