From: soumadwip ghosh (soumadwipghosh_at_gmail.com)
Date: Wed Mar 03 2021 - 00:32:20 CST
Hi,
I have simulated an MSPA protein pore in lipid for 1 ns using steered MD as
shown in the tutorial
https://bionano.physics.illinois.edu/sites/default/files/nanopore-protocols.pdf.
I followed the protocol described in section 3.10 (page 29) for 0.05 V
external field and 1M KCl. However, the current I am getting has negative
values in some of the frames. Is it happening because the system may not be
well equilibrated in such a short time or am I getting such an
ambiguous current because the external field is only 50 mV ? I am showing
below the current_electric.dat file that was produced after executing the
currentTraj.tcl on page 30. Is there anything wrong with the procedure I am
following?
0.075 -16.300602643139975
0.12499999999999999 0.5290047015453344
0.175 1.464401254746031
0.22499999999999998 -0.7136776318778846
0.27499999999999997 -0.01999234528800148
0.32499999999999996 1.2573843539474363
0.37499999999999994 -1.4266596705622407
0.425 -0.3222860406576734
0.475 -0.3000825571992549
0.5249999999999999 -1.2037490289372796
0.575 -1.8169851733662754
0.625 -0.33687052745937707
0.6749999999999999 1.0995286022674309
0.725 0.2529037773776375
0.7749999999999999 2.0539884190047886
0.825 -0.5471836863775636
0.8749999999999999 -0.5362299610804959
0.9249999999999999 0.3134277024231096
0.9749999999999999 2.616593249612792
1.025 0.3470090546120108
1.075 0.590928539300756
1.125 -0.7080767926283599
Thank you for your help in advance.
Best
Soumadwip Ghosh
La Jolla, CA
United States
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