You could use 'constraint' pull-mode instead of the 'umbrella' mode.
Than the distance would change gradually and you won't observe the
fluctuations in the distance.
greetings
thomas
Am 04.10.2012 16:58, schrieb [email protected]:
On 10/4/12 10:52 AM, jiang wrote:
>Justin Lemkul wrote
>>On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote:
>>>Hi Justin,
>>>
>>>I used ~20 windows to sample ~2 nm pulling. I notice that the distance
>>>between the complex being increased during the pulling but not gradually.
>>>At the distance of 0-1nm, there are 70 snapshots (the distance sometime
>>>increased sometimes decreased). At the distance of 1-2nm, there are only
>>>30 snapshots (the distance kept increasing always). At the distance more
>>>than >3nm, the distance increased as 0.3nm of each snapshot, is it normal
>>>and reliable?
>>>
>>
>>I will assume you are using a harmonic potential (umbrella) to do the
>>pulling.
>>In this case, your observations are totally normal. When two species
>>interact
>>strongly, it is harder to pull them apart, thus the spring extends further
>>to
>>induce a larger force before displacement occurs. As the restoring forces
>>are
>>overcome, it is easier to move the pulled group through solution, so it
>>makes
>>more steady progress as the molecules are separated.
>
>
>Hi Justin, it is right I am using umbrella pulling. Now here is another
>hurdle in front of me: How to select the snapshots for umbrella samples?
>Since the distance between two groups went higher or lower at the beginning
>of the pulling. For example, during the pulling simulation, the distance
>changes like:
>0.46 0.42 0.46 0.43 0.44 0.42 0.45 0.44 0.43 0.45 0.44 0.45 0.43 0.44 0.44
>0.54 0.52 0.63 0.65 0.72 0.8 0.92 1.2 1.5 (nm) .....
>I suppose it doesn't matter which snapshots to be chosen, as long as the
>snapshots can indicate a good spacing, the PMF result always should be same,
>right?
>
You need reasonable spacing and sufficient sampling in each window to allow for
proper overlap of the umbrella potentials.
-Justin
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