Rocco Caliandro wrote:
Hi everybody,
I found a discrepancy in the sasa calculation
between gromacs versions 4.0.2 and 4.5.1.
For a trajectory generated by gmx 4.0.2. with AMBER force fiels,
I calculated the sasa values by using the g_sas module taken
from gromacs 4.0.2 (a) and gromacs 4.5.1 (b).
I list the results for three representative residues:
(a) (b)
res 1 0.58 0.35
res 2 1.10 1.05
res 3 0.27 0.05
I got a rough agreement by changing the probe radius
from 0.14 to 0.10 in g_sas from gromacs 5.4.1 (b'):
(a) (b')
res 1 0.58 0.66
res 2 1.10 1.00
res 3 0.27 0.34
Could you explain me the reason for such discrepancy?
Several hundred lines of code are different in between gmx_sas.c between version
4.0.7 and 4.5.3, so I'd suspect something similar in the case of 4.0.2 vs.
4.5.1. Most notably, in 4.0.x, no effort is made to account for periodicity.
-Justin
Cheers,
Rocco
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
