[gmx-users] AFM pulling options

Justin MacCallum jlmaccal at ucalgary.ca
Fri Aug 2 18:28:36 CEST 2002


I've recieved those changes from Marc and will incorperate them when I 
get some time.  The last comment about AFM only working in the z 
directions should no longer be valid and you should be able to pull in 
any direction you like.

One important point for anyone using the pull code:


I've been working on the pull code a little bit at a time and haven't 
been synchronized with the Gromacs release schedule.  The pull code in 
previous releases of Gromacs is probably in some undefined state and 
likely does not work entirely correctly.  Here is a summary of the 
changes I can remember off hand:

1. Output will now be compressed with gzip if option compress is yes.
2. Option "Skip steps" will cause Gromacs to write out n steps. This is 
good for shrinking file sizes.
3. Up to four groups can be pulled, previously you were limitted to two.
4. Umbrella sampling now works.
    Options are:    K1 - K4, which are force constants in kJ/(mol nm-2).
                            Pos1 - Pos4, which are the centers of the 
umbrella potential wrt the reference group.
5. Dynamic reference groups now work with all pulling types instead of 
just constraint force calculations.
6. There is new starting structure generation code.  _This has not been 
tested_, but its on my list of things to do.
7.  AFM, umbrella sampling, and starting structure generation should 
work in parallel, but this has not recieved much testing.

If anyone is willing to test/use any of this, that would be great.  If 
there are any problems, let me know and I'll do my best to correct them 
as quickly as possible.


>Hi again,
>I sent the changes again to Justin. For those who might be interested
>here is a brief summary:
>I added an option 'afmdetail' to the pull parameters, which would lead
>to more detailed output, especially with respect to getting force-extension
>curves out of the simulation. The NEW option is
>afmdetail                = yes
>in pull.ppa.
>- 5 values are output to pull.pdo:
>  Force Springpos pull_grp_pos ref_grp_pos extension
>  where    Force     = k * (Springpos-pull_grp_pos)
>           extension = pull_grp_pos - ref_grp_pos
>- in the Gromacs code for AFM pulling, the refgroup positions are not up-
>  dated. I changed that for the case of afmdetail=yes, so that you can use
>  these coordinates to calculate the extension.
>- Note that the routine that writes AFM data to pull.pdo in Gromacs assumes
>  that you pull in Z direction, as it only writes out the Z components of
>  eg the forces. That is if you pull along y, you will get 0 forces written
>  out although it seems that it was actually pulled along y. This is because
>  the z component of the force is 0 when you pull along y.
>  I couldn't figure out how to change that in a simple way, so even with
>  afmdetail, it only works for Z-direction pulling
>jlmaccal at ucalgary.ca said:
>>>Hi Marc,
>>>which changes were those?  I don't remember getting any, but that
>>>doesnt' mean much ;)
>  Marc Baaden

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