update files

Author: simongravelle

level2/stretching-a-polymer/elongated-box/mdout.mdp

@@ -2,7 +2,7 @@
 ;	File 'mdout.mdp' was generated
 ;	By user: simon (1000)
 ;	On host: laptop
-;	At date: Fri Jun  7 21:13:32 2024
+;	At date: Fri Jun  7 21:13:59 2024
 ;
 ;	Created by:
 ;	                     :-) GROMACS - gmx grompp, 2024.2 (-:
@@ -11,7 +11,7 @@
 ;	Data prefix:  /home/simon/Softwares/gromacs-2024.2 (source tree)
 ;	Working dir:  /home/simon/Git/GROMACS/inputs/level2/stretching-a-polymer/elongated-box
 ;	Command line:
-;	  gmx grompp -f inputs/nvt-peg-h2o.mdp -c em.gro -p topol.top -o nvt -maxwarn 1
+;	  gmx grompp -f inputs/npt-peg-h2o.mdp -c nvt.gro -p topol.top -o npt -maxwarn 1
 
 ; VARIOUS PREPROCESSING OPTIONS
 ; Preprocessor information: use cpp syntax.
@@ -25,7 +25,7 @@ integrator               = md
 ; Start time and timestep in ps
 tinit                    = 0
 dt                       = 0.002
-nsteps                   = 10000
+nsteps                   = 50000
 ; For exact run continuation or redoing part of a run
 init-step                = 0
 ; Part index is updated automatically on checkpointing (keeps files separate)
@@ -147,13 +147,13 @@ tc_grps                  = PEG Water
 tau_t                    = 0.1 0.1
 ref_t                    = 300 300
 ; pressure coupling     
-pcoupl                   = No
-pcoupltype               = Isotropic
+pcoupl                   = c-rescale
+pcoupltype               = isotropic
 nstpcouple               = -1
 ; Time constant (ps), compressibility (1/bar) and reference P (bar)
-tau-p                    = 5
-compressibility          = 
-ref-p                    = 
+tau-p                    = 0.5
+compressibility          = 4.5e-5
+ref-p                    = 1.0
 ; Scaling of reference coordinates, No, All or COM
 refcoord-scaling         = No
 
@@ -173,9 +173,9 @@ annealing-time           =
 annealing-temp           = 
 
 ; GENERATE VELOCITIES FOR STARTUP RUN
-gen_vel                  = yes
+gen-vel                  = no
 gen-temp                 = 300
-gen-seed                 = 65823
+gen-seed                 = -337773065
 
 ; OPTIONS FOR BONDS    
 constraints              = hbonds