Hi, Chris
You can try the &bbmd module for sander.MPI.
The &bbmd is for ABMD with T-REMD and H-REMD. But you can run only T-REMD
by setting the mode='ANALYSIS'. Basically the T-REMD here use
different code from the -rem=1 one, so it should work with NPT ensemble. To
be honest, I don't know if the results will be valid but it is worth trying.
you can check the details of &bbmd here
http://ambermd.org/doc12/nfe.pdf in
section 22.6.5
Best
Feng Pan
On Wed, Dec 21, 2016 at 1:09 AM, Neale, Christopher Andrew <cneale.lanl.gov>
wrote:
> Dear developers:
>
> I have finished including PV work in the T-REMD exchange criterion in
> amber16. I still have an open question about PBC changing too much and the
> fact that "The GPU code does not automatically reorganize grid cells", and
> I'll update this thread if any issues pop up. Note that I did not enable
> pressure coupling Hamiltonian exchange and I completely turned off 2D REMD
> so that I didn't have to worry about passing the other variables around,
> but if you're interested in allowing pressure coupling with REMD then this
> code probably represents a plausible start.
>
> I made modifications to the following files:
> src/pmemd/src/mdin_ctrl_dat.F90
> src/pmemd/src/runmd.F90
> src/pmemd/src/remd_exchg.F90
> src/pmemd/src/cuda/gpu.cpp
>
>
> $ diff amber16/src/pmemd/src/mdin_ctrl_dat.F90
> amber16_pressremdPROPER/src/pmemd/src/mdin_ctrl_dat.F90
> 2152,2157c2152,2157
> < if (ntp .gt. 0) then
> <
> < write(mdout, '(a,a)') error_hdr, 'REMD cannot be run with ntp > 0!'
> < inerr = 1
> <
> < end if
> ---
> > ! if (ntp .gt. 0) then
> > !
> > ! write(mdout, '(a,a)') error_hdr, 'REMD cannot be run with ntp >
> 0!'
> > ! inerr = 1
> > !
> > ! end if
>
>
>
>
> $ diff amber16/src/pmemd/src/runmd.F90 amber16_pressremdPROPER/src/
> pmemd/src/runmd.F90
> 895c895,896
> < si(si_kin_ene) / fac(1),
> print_exch_data, &
> ---
> > si(si_kin_ene) / fac(1), pres0, &
> > si(si_volume), print_exch_data, &
>
>
>
>
>
> $ diff amber16/src/pmemd/src/remd_exchg.F90 amber16_pressremdPROPER/src/
> pmemd/src/remd_exchg.F90
> 68c68,69
> < use pmemd_lib_mod, only : strip
> ---
> > use pmemd_lib_mod, only : strip,mexit
> >
> 158,159c159,162
> < call temperature_exchange(atm_cnt, vel, remd_ptot, my_dim,
> remd_size, &
> < actual_temperature, .true., mdloop)
> ---
> > write(mdout, '(/,a)') ' PV for 2D-REMD not implemented. Exiting.'
> > call mexit(mdout, 1)
> > !call temperature_exchange(atm_cnt, vel, remd_ptot, my_dim,
> remd_size, &
> > ! actual_temperature, .true., mdloop)
> 314a318
> > actual_pressure, actual_volume, &
> 330a335,336
> > double precision, intent(in) :: actual_pressure
> > double precision, intent(in) :: actual_volume
> 340a347,348
> > double precision :: real_pres
> > double precision :: real_vol
> 347c355
> < integer, parameter :: SIZE_EXCHANGE_DATA = 6 ! for mpi_gather
> ---
> > integer, parameter :: SIZE_EXCHANGE_DATA = 8 ! for mpi_gather
> 354a363
> > double precision :: pressurevolumedelta
> 392a402,403
> > my_exch_data%real_pres = actual_pressure
> > my_exch_data%real_vol = actual_volume
> 460a472,480
> > ! * 0.0602214 / 4184 converts units to kcal/mol
> > pressurevolumedelta = &
> > (((ONEKB / my_exch_data%temp0) * &
> > my_exch_data%real_pres) - &
> > ((ONEKB / exch_data_tbl(neighbor_rank+1)%temp0) * &
> > exch_data_tbl(neighbor_rank+1)%real_pres)) * &
> > (my_exch_data%real_vol - exch_data_tbl(neighbor_rank+1)%real_vol)
> * &
> > 0.0602214 / 4184.0
> >
> 465c485,486
> < (my_exch_data%temp0 * exch_data_tbl(neighbor_rank+1)
> %temp0)
> ---
> > (my_exch_data%temp0 * exch_data_tbl(neighbor_rank+1)%temp0)
> &
> > - pressurevolumedelta
> 485,487c506,515
> < write(mdout,'(a8,E16.6,a8,E16.6,a12,f10.2)') &
> < "Metrop= ",metrop," delta= ",delta," o_scaling= ", &
> < 1 / my_exch_data%scaling
> ---
> > write(mdout,'(a8,E16.6,a8,E16.6,a8,E16.6,a5,E16.6,a5,E16.6,
> a5,E16.6,a5,E16.6,a5,E16.6,a5,E16.6,a12,f10.2)') &
> > "Metrop= ",metrop," delta= ",delta, &
> > " pvwrk= ", pressurevolumedelta, &
> > " T1= ", my_exch_data%temp0, &
> > " T2= ", exch_data_tbl(neighbor_rank+1)%temp0, &
> > " P1= ", my_exch_data%real_pres, &
> > " P2= ", exch_data_tbl(neighbor_rank+1)%real_pres, &
> > " V1= ", my_exch_data%real_vol, &
> > " V2= ", exch_data_tbl(neighbor_rank+1)%real_vol, &
> > " o_scaling= ", 1 / my_exch_data%scaling
>
>
>
>
>
> $ diff amber16/src/pmemd/src/cuda/gpu.cpp amber16_pressremdPROPER/src/
> pmemd/src/cuda/gpu.cpp
> 6306,6325c6306,6325
> < if (skin <= 0.5)
> < {
> < printf("ERROR: Calculation halted.");
> < printf(" Periodic box dimensions have changed too much from
> their initial values.\n");
> < printf(" Your system density has likely changed by a large
> amount, probably from\n");
> < printf(" starting the simulation from a structure a long way
> from equilibrium.\n");
> < printf("\n");
> < printf(" [Although this error can also occur if the simulation
> has blown up for some reason]\n");
> < printf("\n");
> < printf(" The GPU code does not automatically reorganize grid
> cells and thus you\n");
> < printf(" will need to restart the calculation from the previous
> restart file.\n");
> < printf(" This will generate new grid cells and allow the
> calculation to continue.\n");
> < printf(" It may be necessary to repeat this restarting multiple
> times if your system\n");
> < printf(" is a long way from an equilibrated density.\n");
> < printf("\n");
> < printf(" Alternatively you can run with the CPU code until the
> density has converged\n");
> < printf(" and then switch back to the GPU code.\n");
> < printf("\n");
> < exit(-1);
> < }
> ---
> > // if (skin <= 0.5)
> > // {
> > // printf("ERROR: Calculation halted.");
> > // printf(" Periodic box dimensions have changed too much from
> their initial values.\n");
> > // printf(" Your system density has likely changed by a large
> amount, probably from\n");
> > // printf(" starting the simulation from a structure a long way
> from equilibrium.\n");
> > // printf("\n");
> > // printf(" [Although this error can also occur if the
> simulation has blown up for some reason]\n");
> > // printf("\n");
> > // printf(" The GPU code does not automatically reorganize grid
> cells and thus you\n");
> > // printf(" will need to restart the calculation from the
> previous restart file.\n");
> > // printf(" This will generate new grid cells and allow the
> calculation to continue.\n");
> > // printf(" It may be necessary to repeat this restarting
> multiple times if your system\n");
> > // printf(" is a long way from an equilibrated density.\n");
> > // printf("\n");
> > // printf(" Alternatively you can run with the CPU code until
> the density has converged\n");
> > // printf(" and then switch back to the GPU code.\n");
> > // printf("\n");
> > // exit(-1);
> > // }
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Thu Dec 22 2016 - 09:00:02 PST
