Re: SMD restrain point in NAMD

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue Aug 04 2009 - 16:55:52 CDT

I wouldn't follow that paper since it is probably outdated. But I think
that both values for k in the paper are correct, just different units. It
is 414 pN/A and 10K_BT/A^2 should yield the same if you plug in the values
for the Boltzman constant and temperature.

Gianluca

On Tue, 4 Aug 2009, snoze pa wrote:

> Gianluca, Thank you for your feedback. I am following the right
> tutorial sent also by you but got confused with the paragraph of the
> paper. Also in same paragraph, they mentioned a force constant of 414
> but down eight lines it says k=10K_BT/A^2.
>
> Regards
> s
>
>
>
> On Tue, Aug 4, 2009 at 1:09 PM, Gianluca
> Interlandi<gianluca_at_u.washington.edu> wrote:
>> The best is if you go through the tutorial:
>>
>> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix.pdf
>>
>> Section 3, in particular 3.2
>>
>> and read also the documentation:
>>
>> http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node41.html
>>
>> The paper you mentioned is from 1999 and I think that NAMD has been updated
>> since than and SMD is implemented in the code of the later NAMD releases. So
>> doing SMD should be more straightforward now.
>>
>> Gianluca
>>
>> On Tue, 4 Aug 2009, snoze pa wrote:
>>
>>> Dear NAMD/SMD users,
>>>
>>> I was going through one of the original paper related to SMD
>>> simulation
>>> http://proteomics.bioengr.uic.edu/papers/1999/1999-unfold-protein.pdf
>>> from Dr. Schulten group. In this paper at page 455, first paragraph
>>> they are discussing about the restrain point movement as
>>>
>>> "To realize a movement of the restraining point with nearly constant
>>> velocity, the position of the restraining point was changed every 100
>>> fs by v t, e.g., 0.05 . The 0.05 stepwise movement of the
>>> restraining point is much smaller than the fluctuation of typical
>>> protein atoms in a 300 K MD simulation, 1 , so this implementation
>>> should not cause an artifact. "
>>>
>>>
>>> How can we set this "the position of the restraining point was changed
>>> every 100 fs by v t" automatically in the NAMD configuration file. I
>>> will highly appreciate your help. I am using standard SMD tutorial
>>> code from
>>> NAMD website. Any script contribution will be of great help.
>>>
>>> Thank you,
>>>
>>> S
>>>
>>>
>>
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>> +1 (206) 685 4435
>> +1 (206) 714 4303
>> http://artemide.bioeng.washington.edu/
>>
>> Postdoc at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     +1 (206) 714 4303
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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