[Fwd: Re: SMD of small molecule dimer]

From: dora guzman (dguzman_at_uci.edu)
Date: Tue May 02 2006 - 11:59:32 CDT

attached mail follows:

Hi Marc,

Thanks for replying. Yes, changing the pulling speed and/or spring
constant yields the same behavior of forces. The dimer is solvated in
chloroform, and has been minimized and equilibrated for over 1 ns. I've
attached a plot where I applied a pulling velocity of 0.5 A/ps and a
spring constant of 555. The H-bonds (in the trajectory) rupture after
approximately 10 A extension (which corresponds to ~30 A in plot).


Marc Q. Ma wrote:

> if you use a smaller or larger pulling speed, and change the spring
> constant, do you get qualitatively same behavior of forces?
> is your dimer solvated? can you share a plot of your results?
> marc
> On Apr 27, 2006, at 8:28 PM, dora guzman wrote:
>> I'm currently using NAMD to run SMD of a small dimer molecule. I
>> using the constant velocity pulling method to calculate the force
>> necessary to pull the two fragments apart, which are only
>> interacting via 6 hydrogen bonds. I would expect that once the
>> hydrogen bonds between the two fragments are ruptured, the force
>> that was built up should rapidly decrease to zero. However, I don't
>> see this happening when analyzing the force-extension curve. Even
>> when the two fragments are very far apart the force does not
>> decrease significantly. Am I calculating the force correctly? I'm
>> using the same procedure in the tutorial,
>> cat filename.log | awk '{if ($1=="SMD") print $0}'> smd.dat
>> then,
>> cat smd.dat | awk '{print $6*nx + $7*ny + $8*nz}'> ft.dat (and the
>> same for calculating extension using columns 3-5)
>> Any advice would be greatly appreciated.
>> Thanks!
>> -dora
> .

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