From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Mon Oct 22 2007 - 08:21:23 CDT
Hi,
Apparently, you have run approximately ten thousand timesteps. That's
too short to sample the stretching of the helix the ABF way, that is,
reversibly. You need on the order of a nanosecond to start having a
broad sampling of the alpha-to-extended transition.
Best,
Jerome
On 10/22/07, Per Jr. Greisen <pgreisen_at_gmail.com> wrote:
> Hi,
>
> In the NAMD documentation for ABF, there is an example for stretching
> deca-alanine. If I apply the input to the configuration file - the alanine
> is not stretched as I would expected from ordinary application of force. The
> ABF gives me the following result:
> 12.100 0.0000 0.0000 0
> 12.300 0.0000 0.0000 0
> 12.500 0.0000 0.0000 0
> 12.700 0.0000 0.0000 0
> 12.900 -0.5639 5.6388 26
> 13.100 -1.1912 0.6341 121
> 13.300 -1.5174 2.6284 139
> 13.500 -1.9330 1.5278 258
> 13.700 -2.3387 2.5289 555
> 13.900 -2.7024 1.1075 1115
> 14.100 -2.8608 0.4774 987
> 14.300 -2.7992 -1.0937 978
> 14.500 -2.6325 -0.5737 957
> 14.700 -2.4741 -1.0104 1174
> 14.900 -2.2683 - 1.0472 1171
> 15.100 -2.0278 -1.3581 930
> 15.300 -1.7928 -0.9914 722
> 15.500 -1.5389 -1.5477 529
> 15.700 -1.2097 -1.7441 257
> 15.900 -0.4726 -5.6270 81
> 16.100 0.0901 0.0000 0
> 16.300 0.0901 0.0000 0
> 16.500 0.0901 0.0000 0
> 16.700 0.0901 0.0000 0
> 16.900 0.0901 0.0000 0
> 17.100 0.0901 0.0000 0
> 17.300 0.0901 0.0000 0
> 17.500 0.0901 0.0000 0
> 17.700 0.0901 0.0000 0
> 17.900 0.0901 0.0000 0
> 18.100 0.0901 0.0000 0
> 18.300 0.0901 0.0000 0
> etc etc
> Can one stretch fx. a peptide using the ABF module? Thanks in advance.
> Best regards
> Per
>
>
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