[gmx-users] help: gromacs mistake

shuai shuai banshuai at gmail.com
Wed Jul 7 18:29:47 CEST 2010

Dear all,

Recently I met a strong error from gromacs. Therefore I would like to know
whether you have experienced the same thing or what is the reason for that.

The system I simulated is nvt MD for N2 (with partial charge) diffusion in a
long tube (100x2.5x2.5 nm^3) at 300k. The problem is that only for some N2
concentration, I get molecules freezed in a small cluster after a few ns. I
was thinking whether PME electrostatic method () does not work stably in
such a long simulation box. The input parameter for PME is shown below.

; Method for doing electrostatics
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r                = 1
epsilon_rf               = 1
; Method for doing Van der Waals
vdw-type                 = Cut-off
; cut-off lengths
rvdw-switch              = 0
rvdw                     = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = No
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Seperate tables between energy group pairs
energygrp_table          =
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no

please help me if you have any suggestions or solutions. many thanks.

best regards
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100707/d892619c/attachment.html>

More information about the gromacs.org_gmx-users mailing list