From: Yi Wang, PhD (dexterwy_at_gmail.com)
Date: Mon Mar 18 2013 - 20:07:26 CDT
Bonjour Jerome,
Yes, that's what I expected initially, and that's why I found it odd when I saw the result. But anyway, that was a few years back and the latest version should not have this issue.
Best,
___________________________
Yi (Yves) Wang, PhD
Chinese Academy of Science
On 2013-3-19, at 上午1:07, Jérôme Hénin wrote:
> 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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