[gmx-users] Replica exchange: Coordinates and simulation box size?

[Johannes Hermann]

Thanks, Justin!

On 23.03.20 17:34, Justin Lemkul wrote:
>
>
> On 3/23/20 12:30 PM, Daniel Burns wrote:
>> Hi Johannes,
>>
>> Somebody please correct me if I'm wrong but I believe it is just the
>> thermostats that are exchanged.
>
> There's a lot of information that is exchanged, including temperature 
> and pressure coupling information, coordinates, velocities, and the box.
>
> static void exchange_state(const gmx_multisim_t* ms, int b, t_state* 
> state)
> {
>     /* When t_state changes, this code should be updated. */
>     int ngtc, nnhpres;
>     ngtc    = state->ngtc * state->nhchainlength;
>     nnhpres = state->nnhpres * state->nhchainlength;
>     exchange_rvecs(ms, b, state->box, DIM);
>     exchange_rvecs(ms, b, state->box_rel, DIM);
>     exchange_rvecs(ms, b, state->boxv, DIM);
>     exchange_reals(ms, b, &(state->veta), 1);
>     exchange_reals(ms, b, &(state->vol0), 1);
>     exchange_rvecs(ms, b, state->svir_prev, DIM);
>     exchange_rvecs(ms, b, state->fvir_prev, DIM);
>     exchange_rvecs(ms, b, state->pres_prev, DIM);
>     exchange_doubles(ms, b, state->nosehoover_xi.data(), ngtc);
>     exchange_doubles(ms, b, state->nosehoover_vxi.data(), ngtc);
>     exchange_doubles(ms, b, state->nhpres_xi.data(), nnhpres);
>     exchange_doubles(ms, b, state->nhpres_vxi.data(), nnhpres);
>     exchange_doubles(ms, b, state->therm_integral.data(), state->ngtc);
>     exchange_doubles(ms, b, &state->baros_integral, 1);
>     exchange_rvecs(ms, b, state->x.rvec_array(), state->natoms);
>     exchange_rvecs(ms, b, state->v.rvec_array(), state->natoms);
> }
>
> -Justin
>
>> A given simulation box's velocities are rescaled accordingly after the
>> exchange and the simulation continues with its own fluctuations in 
>> box size
>> assuming it is pressure-coupled.
>>
>> I don't know anything about incorporating free energy calculations with
>> replica exchange though.
>>
>> Aloha,
>>
>> Dan
>>
>> On Mon, Mar 23, 2020 at 11:07 AM Johannes Hermann 
>> <johannes.hermann at tum.de>
>> wrote:
>>
>>> Dear all,
>>>
>>> I have slightly different Position Restrains and Box sizes over my
>>> lambda windows in an alchemical Free Energy Calculation in NVT ensemble
>>> (I know that my calculated Free Energy Difference will not solely 
>>> depend
>>> on the mutation alone..)
>>>
>>> What happens if I use replica exchange? What exactly is exchanged 
>>> within
>>> different windows: Only the coordinates or also the current simulation
>>> box size?
>>>
>>> Thanks in advance!
>>>
>>> All the best
>>>
>>> Johannes
>>>
>>>
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>
-- 
______________________________________
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 89289 15730
Fax: +49 89289 15714

Email: j.hermann at lrz.tum.de
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