[gmx-users] AFM pulling options
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.
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