[gmx-users] Frozen N2 in a very long tube; was "help: gromacs mistake"

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Jul 7 18:37:40 CEST 2010

Dear shuai shuai:

Please use a descriptive title. I renamed it.

You must describe your problem more. e.g. is the problem that you get  
a frozen cluster in some simulations, or that you don't get this in  
other simulations? What, exactly, is a small cluster of frozen  

You must also give us ALL of your mdp options... e.g. you said NVT,  
but what are your temperature coupling terms?

Finally, you can help yourself here too. You stated that you think  
that this might be related to tube length, so can you please construct  
a shorter tube and see if you can reproduce the problem.


-- original message --

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.

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