[gmx-users] Segmentation fault after merging two equilibrated molecules!

[André Farias de Moura]

Hi Sajjad,

maybe a periodic boundary issue (they seem to be apart in the central
simulation box, but are superimposed with the periodic images of each
other)? try to open the structure with a program that allows periodic
images to be visualized along with the central box to see if there are any
clashes (I'd use VMD for that purpose).

I hope it helps

Andre

On Sat, Jun 4, 2016 at 9:23 AM, Sajjad Kavyani <kavyani.sajjad at gmail.com>
wrote:

> Dear experts,
> I want to simulate a system with a cnt and a molecule passing through it by
> a coarse grained ff.
> First, I ran a nvt (after an em) for a single molecule (no solvent) with no
> problem.
> Second, I do the same with a single cnt and absolutely no problem.
> The problem is where I put them together in a single box. Every time I
> tried that, the "segmentation fault" appears.
> Even in a very large box of 60 nm!!, where they barely see each other to
> interact.
> NOTE: The system has zero charge.
>
> Could someone please explain the situation for me?
>
> The MDP parameter is :
>
> integrator               = md
> tinit                    = 0.0
> dt                       = 0.020
> nsteps                   = 102000
> nstcomm                  = 1
>
> nstxout                  = 5000
> nstvout                  = 5000
> nstfout                  = 0
> nstlog                   = 1000
> nstenergy                = 1000
> nstxtcout                = 1000
> xtc_precision            = 1000
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.2
> coulombtype = cut-off ;PME ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order = 4     ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> rcoulomb_switch          = 0.0
> rcoulomb                 = 1.2
> epsilon_r                = 15
> vdw_type                 = switch
> rvdw_switch              = 0.9
> rvdw                     = 1.2
> DispCorr                 = No
> tcoupl                   = berendsen
> tc-grps                  = system
> tau_t                    = 1.0
> ref_t                    = 300
> Pcoupl                   = no
> compressibility          = 1e-5
> gen_vel                  = no
> gen_temp                 = 320
> gen_seed                 = 473529
> constraints              = none
> constraint_algorithm     = Lincs
> unconstrained_start      = no
> lincs_order              = 4
> lincs_iter              = 1
> lincs_warnangle          = 90
>
>
> (Sorry for the previous wrong subjected mail)
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090