NANMA free energy surface vacuum map problems

From: Carles Corbi Verge (ccorbi_at_ugr.es)
Date: Fri Oct 29 2010 - 08:03:54 CDT

Dear NAMD users,

        I downloaded the files of the ABF tutorial, I started to follow the case 3, isomerization of N-acetyl-N'-methylalanylamide ( NANMA ). With the results files you find in the namd website I try to reproduce the energy surface map of ABF simulations in vacuum. I merged them, then I run the abf_integration script, and The map I get is pretty different to the figure 5.a in the tutorial . The second minima appears in the region [48,52] instead the C7ax region [70,-80] . Is it that possible? Any suggestions?

Best Regards,

Carles Corbi Verge

                                                                      
Departamento de Química Física.
Facultad de Ciencias.
Universidad de Granada.
18071 Granada, SPAIN

Tel: (+34) 958 240437
Fax: (+34) 958 272879

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