[gmx-users] Re: Membrane Runs Crashing

[Neha]

Hi,

Well, I tried running a simulation at ref_p to 1.0 and got the same error as
earlier, so it doesn't seem to be that. That was the only thing I changed in
the mdp file, so I am still not sure as to where the problem is.


Justin Lemkul wrote
> 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
> 
> -- 
> ========================================
> 
> 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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