[gmx-users] Re: Membrane Equilibration

[Neha]

Hi everybody,

Thank you so much for taking the time to read this. 
I thought ref_p would need to be 0.0 and 0.0 if I wanted zero surface
tension. How else could I get a tensionless membrane?

As for the generating velocities, I completely forgot that would ruin the
equilibrium. Would you recommend saying gen_vel = no or simply raising the
gen_temp closer to the required value? If the second how close do you think
I should keep it? Sorry for bombarding you guys with so many questions!

Also no one has commented on this so I'm guessing using the structure file
from the Berendsen run is an okay way to do what I want?

Again thanks for the help!


Justin Lemkul wrote
> On 6/11/13 1:13 PM, HANNIBAL LECTER wrote:
>> ref_p                    = 0.0  0.0 ??
>>
>> Are you sure about this??
>>
> 
> That's a likely culprit.  See below for another.
> 
> 
>>>
>>> On Tue, Jun 11, 2013 at 5:22 PM, Neha <

> nshafique@

> > wrote:
>>>
>>>> Hi everybody,
>>>>
>>>> I am trying to simulate a lipid bilayer and wanted to use Parrinello
>>> Rahman
>>>> coupling. However, I read that Parinello-Rahman is not great for
>>>> equilibration so I thought I would do a small run using the Berendsen
>>>> barostat to decrease the chances of large oscillations. I then used the
>>>> .gro
>>>> file obtained from that run to start a new run using Parrinello-Rahman.
>>>> I
>>>> am
>>>> not sure if that's the correct way to go about doing what I want to do.
>>>>
>>>> My Parrinello run also terminated a little while in, with the error
>>>> that
>>> 2
>>>> of my atoms have moved further apart than the cut-off distance. A part
>>>> of
>>>> my
>>>> mdp file is pasted below and I was wondering if anyone had any
>>> suggestions
>>>> as to stop that from happening. My time step is 0.02 ps and I thought
>>>> increasing tau-p might work. I am using the compressibility from the
>>>> map
>>>> file on the Martini website and am worried that might be too large. Any
>>>> help
>>>> will be super useful! Let me know if you need any more information.
>>>>
>>>>
>>>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
>>>> ; Temperature coupling   =
>>>> tcoupl                   = nose-hoover
>>>> ; Groups to couple separately =
>>>> tc-grps                  = DPPC W
>>>> ; Time constant (ps) and reference temperature (K) =
>>>> tau_t                    = 1.0 1.0
>>>> ref_t                    = 320 320
>>>> nsttcouple               = 1
>>>> ; Pressure coupling      =
>>>> Pcoupl                   = Parrinello-Rahman
>>>> Pcoupltype               = semiisotropic
>>>> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
>>>> tau_p                    = 5.0  5.0
>>>> compressibility          = 3e-4 3e-4
>>>> ref_p                    = 0.0  0.0
>>>> nstpcouple               = 5
>>>>
>>>> ; GENERATE VELOCITIES FOR STARTUP RUN =
>>>> gen_vel                  = yes
>>>> gen_temp                 = 105
> 
> Here is another issue.  You're re-generating velocities (destroying the
> previous 
> equilibration) with a barostat that doesn't usually play nice under such 
> circumstances, and you're generating velocities for a temperature well
> below the 
> target defined in ref_t.  That can cause the thermostat to go haywire,
> which 
> then has negative effects on the pressure (which comes from kinetic energy
> and 
> the virial), which can lead to collapse.
> 
> -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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