update.7 for AMBER v18 addresses this problem. I am not sure if there is a patch for v16 to fix this issue, somebody from the GPU code developers team will need to confirm.
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 1/5/2019 9:40 AM, David Case wrote:
On Fri, Jan 04, 2019, Kung, Ryan wrote:
I am having trouble running restrained MD simulation with pmemd.cuda on
and my restraint file is:
&rst iat=-1,-1, r1=18.6, r2=28.6, r3=28.6, r4=38.6, rk2=10., rk3=10.,
ir6=0, ialtd=0, iresid=0, igr1=6229,6251,6252,6231,6294,6296,
igr2=9515,9516,9519, /
/
Just to be sure: have you installed all updates, especially update.7,
which addresses problems in using COM restraints in pmemd.cuda? Go
to $AMBERHOME, and type "./update_amber --help" for information, and
"./update_amber --update" to get your code up to date. Then, re-run
configure and make.
....dac
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Received on Sat Jan 05 2019 - 07:30:03 PST
