From: Pavan G (pavan.namd_at_gmail.com)
Date: Sun Mar 31 2013 - 12:50:49 CDT
I found a proper solution in this thread.
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2008-2009/3606.html
I seem to have missed this during my search since I was focused too much on
porous media and 2d periodicity. A lipid bilayer separating two different
ion concentrations is essentially the same problem as a porous media
separating water and vapor.
PG
On Fri, Mar 29, 2013 at 9:56 AM, Pavan G <pavan.namd_at_gmail.com> wrote:
> I am trying this out now. Maybe useConstantArea will solve my problem.
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell yes
> useConstantArea yes
>
>
>
>
> On Fri, Mar 29, 2013 at 9:39 AM, Pavan G <pavan.namd_at_gmail.com> wrote:
>
>> Turns out the simulation is not fine. I tested for margins of 0.5, 1.0
>> and 1.5. In all cases water 'leaks' from around the porous media. Some
>> water does go thorough the media as expected. Can somebody comment on how I
>> can prevent this leakage? I expected the x and y images of the porous media
>> will essentially make it an infinite slab preventing any water leakage.
>>
>>
>> On Wed, Mar 27, 2013 at 1:51 PM, Pavan G <pavan.namd_at_gmail.com> wrote:
>>
>>> Hello All,
>>>
>>> I am trying to run a simulation with 3 components; water, porous media
>>> and vapor. Without the vapor region the box dimensions are;
>>>
>>> cellOrigin 36.914 50.465 10.028
>>> cellBasisVector1 98.480 0.000 0.000
>>> cellBasisVector2 0.000 81.957 0.000
>>> cellBasisVector3 0.000 0.000 83.311
>>>
>>> I want to add a 20A vapor region on the +z side of the porous media.
>>> This obviously means that the simulation has to be 2d periodic (in x and
>>> y). To achieve this I removed the 'cellBasisVector3' line and since the
>>> vapor region adds 20A in the z dimension, the center of the box will shift
>>> by 10A along z. So I now have
>>>
>>> cellOrigin 36.914 50.465 20.028
>>> cellBasisVector1 98.480 0.000 0.000
>>> cellBasisVector2 0.000 81.957 0.000
>>> # cellBasisVector3 0.000 0.000 83.311
>>>
>>> I had to remove PME since a sample run failed complaining that PME
>>> requires PBC in all 3 directions (or something on those lines).
>>>
>>> So when I ran this simulation w/o PME and w/o z axis PBC, I got few ps
>>> of data before it died with this error:
>>>
>>> FATAL ERROR: Periodic cell has become too small for original patch grid!
>>> Possible solutions are to restart from a recent checkpoint,
>>> increase margin, or disable useFlexibleCell for liquid simulation.
>>>
>>> I did restart from the last checkpoint and it ran for few more ps and
>>> dies with the same error. useFlexibleCell is already set to 'no'.
>>>
>>> From the forums I found that increasing the 'margin' in the config file
>>> helps. I increased this from default to 1.5. The simulation is running fine
>>> and looks fine as well.
>>>
>>> I am writing to check if my approach is correct. Is this how you would
>>> do it?
>>>
>>> Thank you
>>> PG
>>>
>>
>>
>
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