Hello, thanks for both replies. <div><br></div><div>Properly generalized implementation seems well over my head, so I will settle for a hacked-in solution for my particular case. My bonds will allow re-binding, and I have a reasonable number of them, so I think I am safe in this aspect. I will start working on this and very likely come back with more questions. </div>
<div><br></div><div>But for now, I have one more question : </div><div><br></div><div>Let's say I have a tabulated bond between two particles. The table is as long as the box size (let's say 10 nm) and it is a lj-cos potential so it allows complete dissociation of these two particles. I get an error if these particles get further than some threshold during simulation. I believe that this threshold is due to domain decomposition. I want to have tables as long as the box to allow complete dissociation. This way I will not need any non-bonded interactions for my hydrogen bonds. Would it be possible to ignore this threshold for my "hydrogen bonded" particles?</div>
<div><br></div><div>Particle decomposition comes to mind, but it says "only whole molecules can be assigned to a processor" in the manual, which locks me into a single processor as I have one enormous coarse grained molecule. </div>
<div><br></div><div>Cheers</div><div><br></div><div>Murat<br><br></div><br><div class="gmail_quote">On Thu, Oct 4, 2012 at 4:26 PM, Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
If you want to this completely generally, you would need 3-body non-bonded<br>
interactions. Gromacs is not well suited (yet) for this.<br>
If you have a limited number of hydrogen bonding partners,<br>
you can add a new (or modify) an "angle" potential function in bondfree.c,<br>
this is not to complicated. Then all HB pairs angles should be listed<br>
in your topology and all will be calculated (in parallel possibly not all).<br>
<br>
Cheers,<br>
<br>
Berk<div><div><br>
<br>
On 10/04/2012 02:56 PM, Bogdan Costescu wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi!<br>
<br>
The functions for bonded interactions are all located in<br>
src/gmxlib/bondfree.c. The functions are called on lists of atoms, one<br>
list for one type of interaction potential. The caller already takes<br>
care of splitting the lists between nodes, so you don't have to care<br>
about this aspect. There is however another aspect that comes into<br>
play: what happens after a bond becomes broken. The lists are "fixed",<br>
as the topology is not supposed to change during the MD simulation, so<br>
items from these lists will not magically appear or disappear. If the<br>
bond potential is only based on distance and allows bond reforming,<br>
there is no state to be kept and implementation is quite simple. If,<br>
however, the bond has to remember the state (if it becomes broken it<br>
has to remain broken), there are 2 ways:<br>
- change the lists yourself - they have to be kept synchronized<br>
between nodes, so it becomes a global operation which (if happens<br>
often) will hurt scalability a lot<br>
- keep the state of the bond and move it around with the atoms<br>
whenever the atoms travel between domain decomposition cells<br>
To make things more complex, if you want bonds to break and reform<br>
with different partners, keeping the bond state doesn't help and<br>
changing the lists is the only way.<br>
<br>
In terms of the actual potential, you might find some inspiration in<br>
the cross_bond_bond() and cross_bond_angle() functions in the<br>
bondfree.c file.<br>
<br>
Good luck!<br>
Bogdan<br>
<br>
On Thu, Oct 4, 2012 at 2:28 PM, MURAT OZTURK <<a href="mailto:murozturk@ku.edu.tr" target="_blank">murozturk@ku.edu.tr</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello!<br>
<br>
I am thinking about hacking gromacs in the following way :<br>
<br>
I would like to have an angle potential that would turn on/off depending on<br>
the energy of a particular bond.<br>
<br>
For example, I will have a lennard-jones-cosine potential for a bonded<br>
interaction. This will continuously go to '0' at a threshold. Then I will<br>
have an angle potential between these two atoms (and a third one).<br>
<br>
For each calculation, I would like the angle potential to be multiplied by<br>
the instantaneous value of the bond potential, effectively turning it off if<br>
the bond is 'broken'.<br>
<br>
This is to represent a hydrogen bond in a coarse grained model.<br>
<br>
I have intermediate C/C++ skills (that I haven't used in a while), but I am<br>
intimidated by the parallel nature of the code and am not familiar with the<br>
internals of gmx. I am willing to work on this full time for a week or so.<br>
<br>
I would truly appreciate if someone could comment on the feasibility of this<br>
hack, and possibly show me where to begin.<br>
<br>
Thank you<br>
<br>
Murat<br>
<br>
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