[gmx-users] Re: Potential energy from a previous configuration mismatch

[escajarro]

This is my mdp file for energy minimization:

constraints              = none

; integration parameters
integrator               = l-bfgs
dt                          = 0.00
nsteps                    = 15000

; center of mass removal
nstcomm                  = 10
comm_mode             = Linear

; neighbour searching
nstlist                     = 1
ns_type                  = grid
pbc                        = xyz    
rlist                        = 1.4

; electrostatics
coulombtype              = Reaction-Field-zero
rcoulomb                   = 1.1
epsilon_r                   = 1.0
epsilon_rf                  = 0.0

; van der Waals interactions
vdwtype                  = cut-off
rvdw                       = 1.4          
DispCorr                  = EnerPres     

; Ewald parameters
fourierspacing          = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order              = 4
ewald_rtol               = 1e-6
optimize_fft             = yes

; energy minimization
emtol                    = 0.1
emstep                  = 0.01



And this is the one for MD

constraints              = none

; integration parameters
integrator               = md       
tinit                       = 0
dt                          = 0.001    
nsteps                    = 10000000 
;init_step                = 0
comm_mode            = linear 
nstcomm                 = 10      

; output control
nstxout                 = 10000   
nstvout                 = 10000   
nstfout                  = 0         
nstlog                   = 10000    
energygrps            = hexane-UA ethanol   

; neigbour searching
nstlist                   = 1           
ns_type                = grid        
pbc                      = xyz         
rlist                      = 1.4        

; electrostatics
coulombtype              = Reaction-Field-zero
rcoulomb                   = 1.1
epsilon_r                   = 1.0
epsilon_rf                  = 0.0

; van der Waals interactions
vdwtype                  = cut-off
rvdw                       = 1.4       
DispCorr                  = EnerPres  

; Ewald parameters
fourierspacing           = 0.12
fourier_nx                = 0     
fourier_ny                = 0
fourier_nz                = 0
pme_order               = 4      
ewald_rtol                = 1e-6 
optimize_fft              = yes   

; Generate velocities
gen_vel                   = yes          
gen_temp                = 298.0     
gen_seed                 = -1          


To use as the starting configuration the last configuration of the
minimization, I used the confout.gro file of the minimization as the input
conf.gro for MD. I also tried using the traj.trr file generated after
minimization with the grompp option -t for MD. I used the same top and ndx
files in both simulations.

Thanks



--
View this message in context: http://gromacs.5086.n6.nabble.com/Potential-energy-from-a-previous-configuration-mismatch-tp5003352p5003359.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.