Recovering actual minimum distance from distance.min

[Marcelo Depólo Polêto]

Hi,

I am using Plumed 2.7 along with OpenMM 7.5 to prevent binding of bulk ions to a determined binding site. For that, I am using the script below:

S1: GROUP ATOMS=1452
S2: GROUP ATOMS=1454
BULK: GROUP ATOMS=38391,38393,38395,38397,38399,38401,38403,38405,38407,38409,38411

d1: DISTANCES GROUPA=S1 GROUPB=BULK MIN={BETA=50.}
d2: DISTANCES GROUPA=S2 GROUPB=BULK MIN={BETA=50.}

lwall1: LOWER_WALLS ARG=d1.min AT=0.75 KAPPA=1000.0 EXP=2 EPS=1 OFFSET=0
lwall2: LOWER_WALLS ARG=d2.min AT=0.75 KAPPA=1000.0 EXP=2 EPS=1 OFFSET=0

PRINT STRIDE=1000 ARG=* FILE=COLVAR

I set a safe minimum distance of 0.75nm since binding occurs at 0.35nm. However, a closer look at the trajectory revealed BULK ions at ~0.3nm and COLVAR d1.min and d2.min only show distances higher than 0.65nm.

I realize plumed calculates minimum distances using a continuous function. Is there a way to recover the actual minimum distance?

Best regards,

--

Marcelo Depólo Polêto, Ph.D.

Postdoctoral Associate

Office: 106B Engel Hall

Department of Biochemistry
Virginia Tech

340 West Campus Dr.

Blacksburg, VA 24061

gender pronouns: he/him/his

[Gareth Tribello]

Hello 

Use LOWEST rather than MIN on the distances line.  The value is then d1.lowest.

Gareth

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