[gmx-users] Re: Membrane Runs Crashing
jalemkul at vt.edu
Wed Jun 19 13:12:56 CEST 2013
On 6/18/13 10:12 PM, Neha wrote:
> 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 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
>>> temperatures. I am using a bilayer from the Martini website. I was having
>>> problem with the Parinello-Rahman barostat so I switched to Berendsen and
>>> 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
>>> mdp file, and would love any suggestions as to how to alter it to get
>>> fruitful runs. I am still really new to Gromacs and want to make sure I
>>> 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
>> z-dimension is expanding uncontrollably. Water diffuses faster than the
>> so the z-dimension expands faster than x-y does.
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> gmx-users mailing list
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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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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