[gmx-users] another pull-code question

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Jul 2 18:31:44 CEST 2010

Hi all

Thanks for all the previous information. I have successfully pulled two
molecules together in the manner that  I wished. However  I noticed that
the two molecules both moved. I thought that only pull_group1
should move. I have searched the mailing list and stumbled upon
something about removing the centre of mass motion. I do remove the
centre of mass motion. To keep pull_group0 in place do you set centre of
mass motion = no.

chris.neale at utoronto.ca wrote:
> Sounds correct to me. One can use any method to generate the starting
> conformations. Some methods may yield equilibrium starting structures
> faster than other methods, but they are all ok in principle.
> Nevertheless, as with any simulations, one must ensure that care is
> taken to maintain equilibrium and measure convergence (unless a
> non-equilibrium approach is explicitly desired).
> I also agree that people should be reading your paper  -- although
> maybe they are and I just misinterpreted some of the comments that I
> read. Perhaps it would be less work for you if you simply put in a
> line like "this tutorial is very helpful, but if you try to save an
> hour and skip reading the associated paper then things are likely to
> go terribly wrong somewhere!" .. and if you already have that line,
> then perhaps a larger font ;)
> Chris.
> -- original message --
> I definitely agree.  I think the general point (which I know I've been
> a bit
> off-hand about explaining) is that, if properly applied (key caveat!),
> just
> about any combination of pull method + pull geometry can be used to
> conduct SMD.
>   You're quite right that just trying to shoot some molecule across
> your system
> can have terrible effects for complicated environments.  What I've
> always meant
> is that people shouldn't feel constrained to using only the settings I
> have in
> the tutorial, since they are not the most versatile.
> I think I'll add some discussion on this topic to my tutorial, which
> seems to
> have become quite popular.  I guess I was hoping that people who used the
> tutorial would refer to my paper (from which the tutorial is derived),
> wherein
> we demonstrate that our results were not influenced by the pull rate
> (with both
> k/2 and k/10).  Maybe I should make such things more obvious :)
> -Justin
> chris.neale at utoronto.ca wrote:
>> Hi guys,
>> I just wanted to chime in on the idea that "how you perform the
>> initial pulling to get structures isn't all that important" because I
>> strongly disagree and think that it is, in general, immensely important.
>> OK, it's actually not important if we're talking about pulling two
>> Na+ ions, or two entirely rigid molecules in water, because you are
>> not going to affect their conformations by pulling too quickly.
>> However, let's take the other extreme and say that one wants to
>> generate initial conformations of something in a bilayer or an ion in
>> a membrane channel. In these cases, initial pulling that is too fast
>> can push the bilayer, ligand, or protein so far out of its
>> equilibrium conformation that your US will not sample enough
>> simulation time to re-equilibrate.
>> To sum-up my point of view, the initial pulling simulations should be
>> done as slowly as you can afford, and if you want to have some
>> confidence that your rate is "slow enough", then you should probably
>> run at rate=k and rate=k/10 and check that the starting structures
>> that you get are not separated from each other by huge barriers
>> resulting from some non-equilibrium response at rate=k that was not
>> observed at rate=k/10. Even if you don't go through some procedure
>> like the one above, there is still no need to take risks by limiting
>> your setup pulling simulation to 1 hour of simulation when you're
>> going to then spend the next 2 months doing US (garbage in = garbage
>> out).
>> Chris.

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