From: Pavan G (pavan.namd_at_gmail.com)
Date: Fri Mar 29 2013 - 08:56:33 CDT
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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