From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Mar 18 2013 - 12:07:40 CDT
Hi everyone,
If I may add my little sales pitch to this thread: if you perform SMD as a moving harmonic restraint enforced by the colvars module, it will handle PBC transparently (i.e. distances will be calculated with the minimum image convention).
Cheers,
Jerome
----- Original Message -----
> Jackie,
>
>
> There was one time I got a sudden increase of force: I restarted the
> simulation from a snapshot where the ligand is entering the box from
> the other side because of PBC. Have you checked the structures at
> those timesteps where you got ultrahigh force?
>
>
>
>
>
> ___________________________
>
>
> Yi (Yves) Wang, PhD
> Chinese Academy of Science
>
>
>
>
>
>
>
>
> On 2013-3-16, at 上午1:35, Jacqueline Schmidt wrote:
>
>
>
>
>
> Dear Aron,
> I just learnt the units of force printed by NAMD are PN not
> kcal/mol/Ang. Converting the units, I actually get something close
> to -0.6... I appreciate your comments in any case
>
>
> This amount is just the amount of work done for pulling the peptide
> for ~0.1 or less angstrom away from the surface. I expect the
> overall work or free energy ends up to less than 10-20 kcal/mol...
>
>
> jackie
>
>
>
>
>
>
> From: Aron Broom < broomsday_at_gmail.com >
> To: Jacqueline Schmidt < jacqueline_schmidt_1983_at_yahoo.com >
> Cc: namd < namd-l_at_ks.uiuc.edu >
> Sent: Friday, March 15, 2013 1:10 PM
> Subject: Re: namd-l: smd force is too high
>
>
> Hi Jackie,
>
> I'm not really very familiar with SMD, but have you tried a smaller
> pulling velocity? I can imagine that if the pulling velocity is too
> fast to allow the system to be in a constant pseudo-equilibrium, you
> might appear to have a steeper energy barrier to pulling the protein
> because you have slowly relaxing orthogonal degrees of freedom that
> aren't being given time to relax. That is, you're crossing the
> energy barriers associated with those slowly relaxing degrees of
> freedom using a path that isn't the lowest energy one. Again, I'm
> not terribly familiar with SMD, but this kind of problem is fairly
> general to any biased MD and it will generally present itself as the
> energy barrier appearing to be much greater than you expected.
>
> The above being said, is the value you are getting really that
> extreme? I suppose -0.6 kcal/mol/Ang is effectively the gradient for
> the binding energy? If so, what would you be expecting for the
> actual binding energy over the distance you want to pull? It seems
> like a gradient of this magnitude would only yield a binding energy
> of at most a few kcal/mol or am I confused?
>
> ~Aron
>
>
>
> On Fri, Mar 15, 2013 at 12:25 PM, Jacqueline Schmidt <
> jacqueline_schmidt_1983_at_yahoo.com > wrote:
>
>
>
>
>
> Dear NAMD users,
>
>
> I have a question regarding the smd simulation using NAMD. I am
> pulling off a peptide from a surface (surface is fixed) using smd
> with force constant of 6 kcal/mol/Ang^2 and pulling velocity of
> 5x10^-6 Ang/fs . My problem is the forces that are printed in the
> output are unreasonably highe!
>
>
> e.g. at step 100, the center of mass of peptide has been moved ~0.1
> Ang in z-direction. The smd force printed in the output is fz~-43
> and I assume the units are kcal/mol/Ang
>
>
> but this is so high! Doing a rough calculation for force
> Fz=k(vt-z+z0)= 6(5*10^-6 -0.1) ~-0.6 kcal/mol/Ang
>
>
> can anyone please help me with this?
>
>
> I will appreciate it
> jackie
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
>
>
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