Hello –

This is the APBS discussion list, not the GROMACS discussion list.  Please post your question on the GROMACS forums.

Thank you,

--

Nathan Baker

Laboratory Fellow

Pacific Northwest National Laboratory

+1-509-375-3997

http://www.linkedin.com/in/nathanandrewbaker/

 

From: xuzhiyang614 [mailto:xuzhiyang614@126.com]
Sent: Sunday, September 22, 2013 2:30 AM
To: apbs-users
Subject: [apbs-users] Thanks for your help

 

Dear sir,    

 

      Now, when I do the gromacs using pbc=no , I meet a problem that "Can not have dispersion correction with pbc=no".This is my md.mdp file below.It is my plesure to get your help to solve this problem.Many thanks.

 

title                  = FWS
cpp                    = /usr/bin/cpp
constraints            = hbonds
constraint_algorithm   = LINCS
lincs_order            = 4
comm_mode        = ANGULAR
comm_grps              = protein non-protein 
integrator             = md
dt                     = 0.002 ; ps !
nsteps                 = 2000000 ; total 5000 ps.
nstcomm                = 10
nstxout                = 1000000 ; collect data every 1 ps
nstenergy              = 2000
nstvout                = 1000000
nstlog                 = 1000
nstxtcout              = 2000
xtc_grps               = non-Water
nstfout                = 0
nstlist                = 10
ns_type                = grid
pbc             =    no
coulombtype     = Cut-off
rcoulomb          = 1
rvdw              = 1
fourierspacing         = 0.12
fourier_nx             = 0
fourier_ny             = 0
fourier_nz             = 0
pme_order              = 4
ewald_rtol             = 1e-5
optimize_fft           = yes
energygrps             = Protein Ca SOL
DispCorr               = EnerPres
; Berendsen temperature coupling is on in two groups
Tcoupl                 = V-rescale
tau_t                  = 0.5 0.5
tc-grps                = Protein non-protein
ref_t                  = 300 300
; Pressure coupling is on
;Pcoupl                 = Parrinello-Rahman
Pcoupl          = no
tau_p                  = 1.0
compressibility        = 4.5e-5
ref_p                  = 1.0
; Generate velocites is on at 300 K.
gen_vel                = yes
gen_temp               = 300
gen_seed               = -1

 


pull            = umbrella
pull_geometry   = direction_periodic      ; can't get PMF with direction
pull_dim        = Y N N
pull_start      = yes           ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Pull_1
pull_group1     = Pull_2
pull_vec1       = 1 0 0     ; pull along ARG107 to ARG8
pull_rate1      = 0.005          ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 418.4          ; kJ mol^-1 nm^-2
;pull_group2     =
;pull_vec2       = -1 0 0
;pull_rate2      = 0.01
;pull_k2         = 418.4
pull_nstxout    = 50
pull_nstfout    = 50

 

 

      best wishes                                   

                        

                                           yoursZhiyang Xu(徐志阳)

 

=========================================

 

Zhiyang Xu(徐志阳)
Biomechanics and Biomaterials Laboratory
Department of Applied Mechanics
School of Aerospace Engineering
Beijing Institute of Technology
(北京理工大学-宇航学院)
Beijing 100081, P. R. China
Email: xuzhiyang614@126.com

 

=========================================