Thanks to everybody who helped me out with my last email. But now I have another problem and I hope you can help me. As i told you I'm doing a simulation of polyelectrolyte chain consisting of 50 charged beads (-1) with 50 charged counterions(+1). My box simulation is 400 nm x 400 nm x 400 nm and the polyelectrolyte length is 100 nm. My problem is when I chage the intregator md to bd (position langevin dynamics), it gives me Large VCM (group System) in the md.log file and after some time it crashes at some point. When i take a look at the energy file and plot the temperature I realized that the temperature is far from the desired temperature. Please take a look at my mdp file and help me figure out what i'm doing wrong.
My last question how can I choose the rlist, Vdw and coulomb cut-off when I'm using PME and , for example my case in 400 nm x 400 nm x 400 nm and 100 atoms with fourierspacing = 20 (is it ok?). Thanks in advance.
; By user: pcl
; VARIOUS PREPROCESSING OPTIONS
title = Yo
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = bd
; Start time and timestep in ps
tinit = 0
dt = 0.0001
nsteps = 100000000
comm-mode = Linear
nstcomm = 1
comm-grps = System
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0.05
ld_seed = 1993
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10 ;
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 100
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
;rcoulomb-switch = 0
rcoulomb = 100
fourierspacing = 20
optimize_fft = yes
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 13.89354;
; Method for doing Van der Waals
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 100
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = Berendsen
; Groups to couple separately
tc-grps = NA POL
; Time constant (ps) and reference temperature (K)
tau_t = 0.01 0.01
ref_t = 120.2717 120.2717;
; Pressure coupling
Pcoupl = no
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
; OPTIONS FOR BONDS
constraints = none
--
Cheers,
Paul
National Tsing Hua University (���A��W)
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I appreciate your help. Thanks!
Os agradezco la ayuda. Gracias!
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