From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Thu Jan 22 2009 - 14:17:26 CST
One last thing... with an 8-residue peptide, you probably shouldn't
expect things to converge in 12 ns. ABF is taking care of one phi
angle - convergence depends on what all the other degrees of freedom
are doing.
Jerome
On Thu, Jan 22, 2009 at 1:56 PM, Jorgen Simonsen <jorgen589_at_gmail.com> wrote:
> Hi,
>
>
> I am using
>
> abf xiMin -180.0
> abf xiMax 0.0
>
> with a dxi of 5 I have seen this size of sample in other simulations where
> they got convergence of the angle.
>
> On Thu, Jan 22, 2009 at 6:52 PM, Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
> wrote:
>>
>> Hi Jorgen,
>>
>> I recommend running the calculation in two separate windows (say,
>> [-180:0] and [0:180]). There are several reasons to do that:
>> 1) it's easier to get even sampling in narrower windows
>> 2) you can run them in parallel (linear scaling!)
>> 3) it avoids the behavior where the angle always rotates in the same
>> direction, which gives an asymmetric (and wrong) PMF.
>>
>> Jerome
>>
>> On Thu, Jan 22, 2009 at 12:16 PM, Jorgen Simonsen <jorgen589_at_gmail.com>
>> wrote:
>> > Hi all,
>> >
>> > I have been using the ABF methods in order to estimate some energy
>> > around a
>> > phi-angle in a peptide with 8 residues. I have applied the following
>> > specifications
>> >
>> > fullSamples 5000
>> > dSmooth 0.1
>> > forceConst 1.0
>> >
>> > I have been running the simulation for 12 ns and the distribution is not
>> > uniform and some of the gradients are around -0.15. Is there a way to
>> > speed
>> > up convergence - any comments or suggestions appreciated.
>> >
>> > Thanks in advance
>> >
>> > Jorgen
>> >
>
>
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