From: Per Jr. Greisen (pgreisen_at_gmail.com)
Date: Mon Oct 22 2007 - 06:34:25 CDT
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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