[gmx-users] AFM pulling options

Jian Zou zouj01 at mails.tsinghua.edu.cn
Wed Dec 8 09:04:32 CET 2004


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 
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?

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?

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 

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?

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?

Thank you all in advance.


Jian Zou

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