[gmx-users] Langevin dynamics ( Large VCM )

[PAUL NEWMAN]

Hi:
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 (ÇåÈA´óŒW)

ÖxÖxÄãµÄŽÍæ
I appreciate your help. Thanks!
Os agradezco la ayuda. Gracias!
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