Re: Which conformation is more proper for the SMD

From: Shulin Zhuang (
Date: Mon Jun 09 2008 - 13:21:57 CDT

Hi, Eric,

Great thanks for your so rapid reply. Just as what you suggest, I measure
the Hbond with the criterion: the distance between acceptor and donor pairs
cutoff :3.5 A; donor-H-acceptor angle cutoff is 30 .

My protein has 90 residues. For the whole Hbonds within the protein, the
initial x-ray strucute has 60 Hbond; the minimized strucutre has 71 Hbonds;
after heating the system to 300K, the final heated conformation has 56
Hbond; for the NPT equlibiration, the first 500ps has 55 Hbond; the 1ns
conformation has 49 Hbonds; 1.1 ns conformation has 48 Hbonds; 1.2 ns
conformation has 50 Hbonds; 1.3 ns conformation has 44 Hbonds; 1.4 ns
conformation has 39 Hbonds; for 1.5 ns conformation, it have 56 H bonds in
total. Some times the Hbonds may not be the same in above Hbonds.

I do the equlibration just according to some SMD papers, they often do 1ns
equilibration before starting SMD. Generally compared with the initial
structure, if the backbone RMSD is below 2.0 A, it is ok. For my
case, compared with the x-ray structure, all the equilibrated conformation
has a backbone RMSD belwo 1.2 A, several conformation has a backbone
ofaround 0.9 A. Here I have a question that how long is enough for the
equilibration before SMD. How to effectively judge whether the equilibrated
conformation is right or not. Great thanks!

Best regards

On 6/9/08, Eric H. Lee <> wrote:
> How are you measuring whether a hydrogen bond is present? Are you using
> VMD to visualize them? Keep in mind that one can adjust distance and angle
> cutoffs, and it is best to measure these values manually to confirm that the
> Hbond is actually "broken." If the bond is obviously not viable (such as
> the acceptor donor pairs being separated by say, >3.5A), then it can be
> considered "broken."
> I would actually equilibrate with free dynamics longer (say double the time
> to 3ns total) and observe how this hydrogen bond behaves, in order to
> determine whether it may significantly impact your SMD simulation or not.
> Eric H. Lee
> Medical Scholars Program
> Theoretical and Computational Biophysics Group, UIUC
> On Jun 9, 2008, at 11:43 AM, Shulin Zhuang wrote:
> Dear All,
> Before I perform SMD on my protein, I first equilibrate it for 1ns. Based
> on this 1ns equilibrated conformation, I run another 500 ps. I use the same
> config parameter to do the equilibration on the same linux cluster. For the
> 1ns equilibrated conformation and 1.5 ns conformation, compared with
> x-crystal structure, these two conformation have a backbone RMSD of 0.9.
> The backbone RMSD between this two conformation is 0.7. However, compared
> with the x-crystal structureI find that in 1.5 ns equilibrated conformation,
> one backbone hydrogen bond is lost, while in the 1ns equilibrated
> conformation, no backbone hydrogen bond is lost. Here I wonder if the 1.5ns
> equilibrated conformation is right or not, should I only use the 1ns
> equilibrated conformation for the SMD? Thanks a lot!
> Best regards
> Shulin

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