[gmx-users] Membrane Runs Crashing

[Justin Lemkul]

On 6/18/13 3:13 PM, Neha wrote:
> Hi everybody!
>
> I am trying to simulate a lipid membrane at zero pressure and at a range of
> temperatures. I am using a bilayer from the Martini website. I was having a
> problem with the Parinello-Rahman barostat so I switched to Berendsen and am
> also keeping the height of the box constant otherwise it grows
> uncontrollably. However my runs keep crashing, giving the error of atoms
> having moved too far beyond the cut-off distance. I have attached part of my
> mdp file, and would love any suggestions as to how to alter it to get more
> fruitful runs. I am still really new to Gromacs and want to make sure I am
> not doing something completely wrong.
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; Method for doing electrostatics =
> coulombtype              = Shift
> rcoulomb_switch          = 0.0
> rcoulomb                 = 1.2
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon_r                = 15
> ; Method for doing Van der Waals =
> vdw_type                 = Shift
> ; cut-off lengths        =
> rvdw_switch              = 0.9
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr                 = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> ; Temperature coupling   =
> tcoupl                   = Berendsen
> ; Groups to couple separately =
> tc-grps                  = DPPC W
> ; Time constant (ps) and reference temperature (K) =
> tau_t                    = 1.0 1.0
> ref_t                    = 325 325
> ; Pressure coupling      =
> Pcoupl                   = berendsen
> Pcoupltype               = semiisotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p                    = 1.0  1.0
> compressibility          = 5e-6 0.0
> ref_p                    = 0.0  0.0
>
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel                  = yes
> gen_temp                 = 325
> gen_seed                 = 473529
>
> Please let me know!
>

What happens if you set ref_p to 1.0?  I don't understand the use of zero 
pressure; your system is expanding out into a vacuum and that's likely why the 
z-dimension is expanding uncontrollably.  Water diffuses faster than the lipids, 
so the z-dimension expands faster than x-y does.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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