[gmx-users] Re: Membrane Runs Crashing

[Justin Lemkul]

On 6/18/13 10:12 PM, Neha wrote:
> 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.
>

Please post a full .mdp file; partial .mdp files are rarely useful.

-Justin

>
> 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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> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Runs-Crashing-tp5009264p5009271.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
========================================

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

========================================