Hello,
I want to run umbrella sampling simulations of moving a ligands from one location in the protein to another. There is a clear reaction coordinate the can be expressed as a linear combination of two distance, e.g., D1-D2.
I set up a run using a restraint approach described in this input section:
&wt type='DUMPFREQ', istep1=10, /
&wt
type='END'
/
DISANG=step7_production.rest
DUMPAVE=dist_vs_t.dat
LISTIN=POUT
LISTOUT=POUT
&end
The .rest file looks like this:
&rst
iat=5823, 8439, 8439, 5281,
rstwt = 1,-1,
r1=-10.75, r2=-10.25, r3=-10.25, r4=-9.75,
rk2=100.0, rk3=100.0,
/
The question is whether I can run it in pmemd.cuda, or even pmemd.MPI?
So far I have only succeeded in running it in sander.MPI and it is rather slow.
We have AMBER20 and are using a large cluster at Mount Sinai (Minerva) both with CPU and GPU capbilites.
Thank you for your help.
Roman Osman
Professor
Department of Pharmacological Sciences
Icahn School of Medicine at Mount Sinai
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 18 2022 - 12:30:03 PST
