Dear Amber users,
I am looking at using tREMD simulations to study the aggregation of small molecules. Initially, when running tREMD simulations in implicit solvent, the molecules disperse, whereas in standard MD they aggregate. To overcome this I though I could use some restraints and have been using a restraint file which has pairs of restraints between all molecules (e.g. below for 4 residues).
However when applied to larger systems with multiple replicas I tend to get a coordinate resetting error for some of the replicas.
Is there anyway to overcome this?
Juliette
&rst iat =-1,-1, igr1 = 1,40, igr2 = 41,80,
r1 = 0.01, r2 = 25, r3 = 25, r4 = 35, rk2 = 0.01, rk3 = 6,
r1a = 0 r2a = 25, r3a = 25, r4a = 35, rk2a = 0.01, rk3a = 6,
/
&rst iat =-1,-1, igr1 = 1,40, igr2 = 81,120,
r1 = 0.01, r2 = 25, r3 = 25, r4 = 35, rk2 = 0.01, rk3 = 6,
r1a = 0 r2a = 25, r3a = 25, r4a = 35, rk2a = 0.01, rk3a = 6,
/
&rst iat =-1,-1, igr1 = 41,80, igr2 = 81,120,
r1 = 0.01, r2 = 25, r3 = 25, r4 = 35, rk2 = 0.01, rk3 = 6,
r1a = 0 r2a = 25, r3a = 25, r4a = 35, rk2a = 0.01, rk3a = 6,
/
&rst iat =-1,-1, igr1 = 1,40, igr2 = 121,160,
r1 = 0.01, r2 = 25, r3 = 25, r4 = 35, rk2 = 0.01, rk3 = 6,
r1a = 0 r2a = 25, r3a = 25, r4a = 35, rk2a = 0.01, rk3a = 6,
/
&rst iat =-1,-1, igr1 = 41,80, igr2 = 121,160,
r1 = 0.01, r2 = 25, r3 = 25, r4 = 35, rk2 = 0.01, rk3 = 6,
r1a = 0 r2a = 25, r3a = 25, r4a = 35, rk2a = 0.01, rk3a = 6,
/
&rst iat =-1,-1, igr1 = 81,120, igr2 = 121,160,
r1 = 0.01, r2 = 25, r3 = 25, r4 = 35, rk2 = 0.01, rk3 = 6,
r1a = 0 r2a = 25, r3a = 25, r4a = 35, rk2a = 0.01, rk3a = 6,
/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:38:08 PDT
