-
Notifications
You must be signed in to change notification settings - Fork 57
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Add interface test for gromacs 2024 with no config
- Loading branch information
1 parent
14281bc
commit 27d2a13
Showing
2 changed files
with
71 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,56 @@ | ||
;Run control | ||
integrator = md | ||
;time step in picoseconds | ||
dt = 0.001 | ||
;number of steps | ||
nsteps = 20 | ||
;frequency to write coordinates to output trajectory file | ||
nstxout = 1 | ||
nstvout = 1 | ||
nstfout = 1 | ||
;frequency to write energies to log file | ||
nstlog = 1 | ||
;frequency to write energies to energy file | ||
nstenergy = 1 | ||
nstcalcenergy = 1 | ||
;frequency to write coordinates to xtc trajectory | ||
nstxout-compressed = 1 | ||
|
||
;Frequency to update the neighbor list (and the long-range forces, | ||
;when using twin-range cut-off's). | ||
nstlist = 10 | ||
ns_type = grid | ||
|
||
;cut-off distance for the short-range neighbor list | ||
rlist = 1.4 | ||
cutoff-scheme = verlet | ||
|
||
|
||
|
||
;treatment of van der waals interactions | ||
vdwtype = cut-off | ||
vdw-modifier = Potential-switch | ||
rvdw = 1.2 | ||
rvdw-switch = 1.0 | ||
|
||
;treatment of electrostatic interactions | ||
;coulombtype = Reaction-Field-zero | ||
rcoulomb-switch = 1.0 | ||
rcoulomb = 1.2 | ||
|
||
;Constrain h-bonds with SETTLE | ||
;Match NAMD parameters | ||
constraints = h-bonds | ||
constraint-algorithm = SHAKE | ||
|
||
; comm_mode = Angular | ||
|
||
; Periodic boundary conditions | ||
pbc = xyz | ||
;Temperature coupling | ||
tcoupl = no | ||
;Velocity generation | ||
gen_vel = no | ||
|
||
; Colvars configuration | ||
colvars-active = yes |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,15 @@ | ||
# -*- sh-basic-offset: 2; sh-indentation: 2; -*- | ||
|
||
# For GROMACS 2024 with Colvars MdModule | ||
|
||
gmx_d grompp -f nocvconfig.mdp -c ../Common/system.gro -p ../Common/system.top -o test.tpr | ||
# Restart tpr | ||
gmx_d convert-tpr -s test.tpr -o test.restart.tpr -nsteps 100 | ||
|
||
|
||
basename=test | ||
options="-ntmpi 1 -ntomp 2" | ||
|
||
gmx_d mdrun -s test.tpr -deffnm ${basename} ${options} &> ${basename}.out | ||
|
||
gmx_d mdrun -s test.tpr -deffnm ${basename} -noappend -cpi ${basename%.restart}.cpt -colvars_restart test.colvars.state.dat ${options} &> ${basename}.out |