From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed May 06 2009 - 11:04:21 CDT
Thanks Anton for your answer.
Any ideas how it affects the stability of a simulated protein? If for
example I'm simulating a protein at 300 K starting from its X-ray
structure, is it going to appear less fluctuating with a larger damping
coefficient (e.g., 10/ps versus 5/ps)? In other words, it's going to slow
down conformational sampling?
Thanks,
Gianluca
On Wed, 6 May 2009, Anton Arkhipov wrote:
> Hi Gianluca,
>
> The damping coefficient introduces friction, so it does influence an MD
> simulation. In principle, you want to set the damping coefficient as low as
> possible, because if its value is high, atoms will experience too much
> unnatural friction. However, you cannot make the coefficient too low, because
> in that case your system will fluctuate too far away from the temperature you
> want.
>
>> How much does for example a value of 10/ps slow down dynamics versus a
>> value of 5/ps?
>
> Friction is going to be 2 times stronger.
>
> I saw some people using the damping coefficient as low as 0.5 ps^(-1), and
> like you said as high as 10 ps^(-1). In my opinion, 5 ps^(-1) is probably the
> highest value one can use for an all-atom simulation. The reason is that with
> damping coefficient set to 0, water diffusion (for TIP3P) is a few times
> faster than it should be (compared to experimental measurements), while
> experience in our group shows that using 5 ps^(-1) results in the water
> diffusion coefficient being close to the experimental value. So, if you are
> using damping coefficient higher than 5 ps^(-1), you water diffusion is going
> to be slower than it should be.
>
> On the other hand, even though 5 ps^(-1) gives you water diffusion that is
> about right, it may slow down other processes. So it still might be too high.
> I personally have been using 2 ps^(-1) for a while, and it seems to work
> pretty well, even though water may diffuse a bit too fast.
>
> Anton.
>
>
> On 5 May 2009, at 16:49, Gianluca Interlandi wrote:
>
>> How strongly does the Langevin damping coefficient influence a molecular
>> dynamics simulation?
>>
>> After quickly browsing the literature I see that values between 1/ps and
>> 10/ps are used where most people use 5/ps. How much does for example a
>> value of 10/ps slow down dynamics versus a value of 5/ps?
>>
>> Thanks,
>>
>> Gianluca
>
>
-----------------------------------------------------
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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