[gmx-users] Re: [gmx-usersDigest] AFM pulling options

Justin MacCallum jlmaccal at ucalgary.ca
Thu Dec 9 10:30:35 CET 2004

> Today's Topics:
>    1. AFM pulling options (Jian Zou)
>    2. Re: Re: Gromacs can't run on AIX system! (Florian Haberl)
> From: "Jian Zou" <zouj01 at mails.tsinghua.edu.cn>
> Subject: [gmx-users] AFM pulling options
> Hi,
> I am now trying to simulate pulling a peptide for 1 ns with gromacs 3.2.1.
> I checked the manual v3.2 and found that the "afm_rate" is in nm/ps, while
> from my former's .ppa who used gromacs 3.1.4, and found the rate is in
> nm/timestep.
> In my case, I choose 0.0001 for "afm_rate" first but found it is too fast,
> then I change to 0.00001 and found the speed is ok. I wonder if the unit for
> "afm_rate" is really nm/ps for gromacs 3.2.1 or it is just a typo?

I'm pretty sure its a typo.

> The second question is related to the "afm_k".
> Could someone tell me how this force constant value influence the pulling
> process? the larger the better? In my case, I should restrain some part of
> my system. Should I choose the force constant in the itp file bigger than
> this k value of AFM?

Obviously the higher force constant you use, the stiffer the spring. I
generally use a very stiff force constant so that the pulled group follows the
spring very closely. But, I'm also using a very slow pull rate. I'm not sure
exactly what you're trying to do, so I won't comment on what would be
appropriate for your system.

> The third question is about "reference_group".
> The manual v3.2 says that if the "reference_group" is left blank, then the
> pulling is performed in absolute coordinates. I tried this but errors
> occured. While I fill in some group for "reference_group", the simulation
> can be performed. It seems that "reference_group" cannot be left blank or I
> should simply remove this line from the ppa file? I asked someone else about
> this and their conclusion for leaving the "reference_group" blank is the
> same.

Removing this line is the same as having it blank. I'm not sure exactly what
the problem is, but I believe there is a bug in the absolute coordinate
reference. I believe someone posted a fix earlier. I'm not sure if its been
fixed in CVS or not.

> The fourth question is about "afm_init".
> The manual says that to start a simulation with zero init force on the
> pulled group, init position should be set to the position of the pulled
> group relative to the ref group. The position of one group to another is the
> center of mass vector of these two group? If the reference group is(or could
> be) set to be the absolute coordinates, the afm_init should be just the
> position of the c.o.m, am I right?

Yes it is the COM vector between the pulled and reference group. In the case
of absolute reference, the value for afm_init will just be the position of the
pulled group.

> The last question is about how to choose the pulling group.
> Should I make in the ndx file a group containing only the terminal atom or
> the atomic group? Which will be more convenient?

This is entirely up to you. I have usually been pulling an entire molecule so
I simply use the COM of the whole molecule. I've also pulled on parts of a
protein. In that case we simply pulled on the COM of a group of selected

> Thank you all in advance.
> Regards,
> Jian Zou

Justin MacCallum
PhD Student
Department of Biological Sciences
University of Calgary
jlmaccal at ucalgary.ca

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