I suggest running the simulation at a single T (not REMD) at the
temperature of your highest T in the REMD simulation. it might be easier to
debug. Do you get the error? Make sure normal MD works before moving to
REMD.
also I am not sure you need to define the "a" variables in the restraints
if they are not changing.
also look closely at your rk2 and rk3 values to make sure the resulting
function is what you want.
On Thu, Aug 4, 2022 at 10:15 AM Juliette Newell via AMBER <amber.ambermd.org>
wrote:
> 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,
> /
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Received on Thu Aug 04 2022 - 13:38:09 PDT
