From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Wed May 06 2009 - 11:13:13 CDT
Gianluca,
Yes, I think that a higher damping constant will indeed slow down
conformational sampling. That's why one wants to use a low value for
the damping constant, in principle.
Anton.
On 6 May 2009, at 11:04, Gianluca Interlandi wrote:
> 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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