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From: Stregone <stregone.protonmail.com>

Date: Wed, 17 May 2017 14:06:07 -0400

Good evening AMBER community,

I would like to perform a EVB/LES-PIMD simulation in order to estimate kinetic isotope effects.

The reaction is SN2 and 2 atoms + 2 molecules are involved in the reaction

As I am starting from the scratch, first I need to create a periodic box with the reactans. As the reaction occurs in water I need to equilibrate the system. Here surges my 1st question^.

Do I need to freeze the the atoms involved in the reaction in order to prevent them to spread along the periodic box or it does not matter ?

At the beginning I had the problem with MD equil. so I had to use [fixatomorder] in order to equilibrate the system. Later I realised that, the reactants kind of spread far from each other.

I know that later on in the simulation, during the EVB/LES-PIMD, the umbrella sampling will be used, so really this spreading atom issue is

insignificant, but I would like to be sure.

In case that I need to freeze the atoms, I assume that I should use ibelly. would this input be correct

NPT simulation of SUR

&cntrl

imin = 0,

irest = 0, ntx = 1,

ntb = 2, cut = 10.0,

ntc = 2, ntf = 2, ! Shake hydrogen atoms

ntp = 1,taup = 3.0, pres0 = 1.013,

tempi = 298.15, temp0 = 298.15,

ntt = 1, ig = -1,

nstlim = 600000, dt = 0.0005,

ntpr = 200, ntwx = 200, ntwr = 200,

iwrap = 1, ! wrap periodic molecules back into box

ibelly = 1, !subset of the atoms in the system will be allowed to move, and the coordinates of the rest will be frozen

bellymask=’.11-9517’, !(atoms in residues 1-58 to move)

/

Before calculating kinetic isotope effects, I need to run a PIMD simulation (based on the manual AMBER 14).

Then I can perform 2 separated thermal integrations. 1st the EVB/LES-PIMD in the reactant region, where

clambda change from 0 to 1 (I have experience in this part). However the 2nd calculation,

along the dividing surface (TS) is not quite clear for me. Based on what I understood (pag. 468),

in the second TI , I already should have found the dividing surface (TS).

Which means that before performing such simulation, I would need to run Path integral quantum transition state theory,

and only then, I could run the 2nd TI, along the dividing surface (TS).

Or , during the 2nd TI, the Path integral quantum transition state theory will be performed along with

isotope calculation. Quote " Sampling of dVeff /dλ along the dividing surface is invoked in a similar fashion,

but with ground-state dynamics replaced by biased sampling constrained to the dividing surface"

Because it gives the sense of performing all together. In that case the commands would look like this ???

evb_dyn = “dbonds_umb”, dbonds_umb(1)%iatom = 8, !TS

dbonds_umb(1)%jatom= 9, dbonds_umb(1)%katom = 7, !TS

dbonds_umb(1)%k = 400.000, dbonds_umb(1)%ezero = 0.0 !TS

ievb=1, ipimd=2, ntt=4, nchain=4, itimass=1, clambda=0.2, !IE

Thanks

Best Regards,

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed May 17 2017 - 11:30:02 PDT

Date: Wed, 17 May 2017 14:06:07 -0400

Good evening AMBER community,

I would like to perform a EVB/LES-PIMD simulation in order to estimate kinetic isotope effects.

The reaction is SN2 and 2 atoms + 2 molecules are involved in the reaction

As I am starting from the scratch, first I need to create a periodic box with the reactans. As the reaction occurs in water I need to equilibrate the system. Here surges my 1st question^.

Do I need to freeze the the atoms involved in the reaction in order to prevent them to spread along the periodic box or it does not matter ?

At the beginning I had the problem with MD equil. so I had to use [fixatomorder] in order to equilibrate the system. Later I realised that, the reactants kind of spread far from each other.

I know that later on in the simulation, during the EVB/LES-PIMD, the umbrella sampling will be used, so really this spreading atom issue is

insignificant, but I would like to be sure.

In case that I need to freeze the atoms, I assume that I should use ibelly. would this input be correct

NPT simulation of SUR

&cntrl

imin = 0,

irest = 0, ntx = 1,

ntb = 2, cut = 10.0,

ntc = 2, ntf = 2, ! Shake hydrogen atoms

ntp = 1,taup = 3.0, pres0 = 1.013,

tempi = 298.15, temp0 = 298.15,

ntt = 1, ig = -1,

nstlim = 600000, dt = 0.0005,

ntpr = 200, ntwx = 200, ntwr = 200,

iwrap = 1, ! wrap periodic molecules back into box

ibelly = 1, !subset of the atoms in the system will be allowed to move, and the coordinates of the rest will be frozen

bellymask=’.11-9517’, !(atoms in residues 1-58 to move)

/

Before calculating kinetic isotope effects, I need to run a PIMD simulation (based on the manual AMBER 14).

Then I can perform 2 separated thermal integrations. 1st the EVB/LES-PIMD in the reactant region, where

clambda change from 0 to 1 (I have experience in this part). However the 2nd calculation,

along the dividing surface (TS) is not quite clear for me. Based on what I understood (pag. 468),

in the second TI , I already should have found the dividing surface (TS).

Which means that before performing such simulation, I would need to run Path integral quantum transition state theory,

and only then, I could run the 2nd TI, along the dividing surface (TS).

Or , during the 2nd TI, the Path integral quantum transition state theory will be performed along with

isotope calculation. Quote " Sampling of dVeff /dλ along the dividing surface is invoked in a similar fashion,

but with ground-state dynamics replaced by biased sampling constrained to the dividing surface"

Because it gives the sense of performing all together. In that case the commands would look like this ???

evb_dyn = “dbonds_umb”, dbonds_umb(1)%iatom = 8, !TS

dbonds_umb(1)%jatom= 9, dbonds_umb(1)%katom = 7, !TS

dbonds_umb(1)%k = 400.000, dbonds_umb(1)%ezero = 0.0 !TS

ievb=1, ipimd=2, ntt=4, nchain=4, itimass=1, clambda=0.2, !IE

Thanks

Best Regards,

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed May 17 2017 - 11:30:02 PDT

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