Re: [Fwd: Re: SMD of small molecule dimer]

From: Marc Q. Ma (
Date: Tue May 02 2006 - 14:27:18 CDT

Hi Dora,

Sorry for getting back to you late. Here is my $.02

1. Depends on how you pull your system, you may be observing the
resistance from the solvent.

2. To see this, I'd suggest you solvate your system using a long and
narrow box of water, and pull the first NH group on each end of your
monomer. you will probably two pronounced peaks, one corresponding to
having 6 H-bonds, the 2nd corresponding to having two H-bonds.

3. If you think the rupture above is not the physics you are
interested in, you could do
  a. remove the solvent, and use Langevin forces to partially recover
some solvent effect, or
  b. have a huge water box
  c. fix all heavy atoms in one monomer, and pull the R2O group as
you did before, this way you may observe a few peaks corresponding to
rupture of 1-6 hydrogen bonds.

thus, depending your research design, you may come up with a few
schemes that each has its own pros/cons.

please let the list know how you solve your problems finally ....


On May 2, 2006, at 12:59 PM, dora guzman wrote:

> From: dora guzman <>
> Date: May 1, 2006 6:39:20 PM EDT
> To: "Marc Q. Ma" <>
> Subject: Re: namd-l: SMD of small molecule dimer
> 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).
> -dora
> 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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