[gmx-users] problem in pulling in gromacs 4.03

[Berk Hess]

Hi,

I think this is a bug in 4.0.3.
Please switch to 4.0.4.

Berk


Date: Sat, 4 Apr 2009 22:00:44 +0530
From: polley.anirban at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] problem in pulling in gromacs 4.03

Dear sir,
            I want to pull a small protein molecule (GPI) which is inserted on the upper layer of the bilayer. So, I applied pull = umbrella, where umbrella potential is used between center of mass of reference group and that of pulled group. Now, as I want to pull the protein from the lipid bilayer membrane, I use the whole molecule of protein as pulled group and the whole patch of bilayer as a reference group because I thought that though I write the whole patch of bilayer as a reference group, the pull will occur w.r.t. the center of mass of the reference group. It will create no problem. Similarly, I did for the whole protein as a pulled group.

            I tried the pull_geometry as all distance, direction, position and it does not give any error during simulation. But, when I saw the whole trajectory in VMD, then I saw that the protein did not come out by the pulling. It is just vibrating at the same position.

            When I ran the simulation in NVT ensemble, the bilayer still retain its structure but when I ran it in NPT  ensemble, it created crazy things, water entered inside, lipids became shrinked and so on.
            Can you please help me and tell me how to do it? I am eagerly waiting for your help.


;
 
title                =  lipid bilayer in water
cpp                  =  /lib/cpp
 
integrator           =  sd              ; stochastic dynamics -> Langevin!
ld_seed              =  -1              ; random seed for sd 

dt                   =  0.002           ; ps !
nsteps               =  250000          ; total 500 ps
nstcomm              =  1               ; freq. for cm-motion removal
tinit                =  0               ; starting time (ps)

 
constraints          =  all-bonds       ; constraint for all bond lengths
constraint_algorithm =  lincs           ; default
lincs_order          =  4               ; default
 
nstxout              =  5000            ; T(x_out) 10 ps

nstvout              =  5000            ; T(v_out) 10 ps
nstfout              =  0               ; T(f_out)
nstlog               =  250             ; energies to log (0.5 ps)
nstenergy            =  250             ; energies to energy file

 
ns_type              =  grid            ; nl type
nstlist              =  10              ; Freq. to update neighbour list
rlist                =  1.0             ; nm (cutoff for short-range nl)
 
coulombtype          =  PME             ;Reaction-Field  ; Coulomb interactions

rcoulomb             =  1.0             ;2.0             ; nm (Coulomb cut-off!!)
epsilon_r            =  80.0            ; dielectric constant for reaction field
vdwtype              =  Cut-off         ; Wan der Waals interactions

rvdw                 =  1.0             ; nm (LJ cut-off)
optimize_fft         =  yes 

; Temperature coupling
Tcoupl               =  no              ; no effect when integrator = sd
tc-grps              =  DPP   SM   CHOL   SOL  GPI     

tau_t                =  0.1   0.1   0.1   0.1   0.1
ref_t                =  310   310   310   310   310
 
; Pressure coupling
Pcoupl = no
;Pcoupl               =  berendsen
Pcoupltype           =  semiisotropic

tau_p                =  1.0    1.0       ; ps
compressibility      =  4.5e-5 4.5e-5    ; 1/bar (water: 1 atm, 300 K)
ref_p                =  1.0    1.0       ; bar
 
; Generate velocites in the beginning
gen_vel              =  yes 

gen_temp             =  310.0
gen_seed             =  173529 


;............................................................................................................
;pulling
pull = umbrella
pull_geometry = direction

pull_start = yes
pull_ngroups = 1
pull_group0 = DPP
pull_group1 = GPI  
pull_dim = N N Y
pull_k1 = 100
;pull_kB1 = 500
pull_rate1 = 0.0005
pull_vec1 = 0 0 1
pull_init1 = 0.0
pull_nstxout = 1   



Thanking you,
Anirban

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