Dear users,
I would like to carry out steered molecular dyanmics simulations on one of
my protein dimer. I have a few questions to learn regarding this.
1. The mdrun program needs -pn index.ndx file
The way I understand is, we need to create the index file with groups (say
atom1 to which the spring has to be attached and the atom 2 which I would
like to fix). These are the names (I mean what ever the names I give for the
groups in the index file) do I need to mention at group_1 and group_2 in
pull.ppa ??
yes, read the manual.
I believe the index file can be prepared in the same way as we
do in conventional MD simulations.
yes, in fact if you put group0 and group1 in your original .ndx file
then you can use the same .ndx for -n and -pn
2. Its a general question. What usually the rates people does use for spring
motions ?
As slow as possible while still finishing the simulation within a
reasonable amount of time.
3. I donot have experimental AFM studies on my system so how can I choose
the optimum force ?
That depends on your system and it's properties. I don't know of any
general rule. I suggest that you try 500 kcal/mol/nm^2 with a fairly
quick pulling (finish in one day of run-time?) and see if you do
eventually obtain your target end state. If you do, then the Fc is
probably high enough.
4. I want to pull the atom along the "Z" direction. I belive afm_dir1 = 0 0
1
Yes.
5. How can I mention the initial spring positoins ?? i.e., afm_init1 ??
I looked for a few tutorials on this but i do not have any luck. If somebody
finds some stuff regarding this could you please share the links with me ??
The manual gives you all of this information. Check the online manual
under .mdp options for a quick description.
Thanks.
You are clearly using gromacs 3. Please note that gromacs 4 has a
different input parameter method (but you can read the manual to see
differences when you get to gmx 4).
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