[gmx-users] Re: Targeted MD

[Stanislav Bobritsky]

>Stanislav Bobritsky wrote:
>>* Hello dear gromacs users!
*>*> I`m trying to do targeted MD. I have two protein conformations which are

*>*> different from each other by one loop position. I need to force
*>*> conformation A to B.
*>*> It was following commands executed:
*>*>
*>*> grompp -с box.gro -f
md.mdp -r conf1.pdb -rb conf2.pdb -p topol.top -o
*>*> transformer.tpr
*>*>
*>*
> mdrun -s transformer.tpr -o -x -c -e -g -v
*>*>
*>*> But it can be viewed from traj.xtc that conformation didn`t change.

*>*> Protein just spins (with speed increasing), and desired loop does not move.
*>*>
*>*
> What can I do to fix it?
*>
>What's in your .mdp file?
>
>Mark

.mdp file contains following:

title                    = prot
cpp                     = cpp
define                 = -DFLEX_SPC

integrator            = md
tinit                    = 0
dt                       = 0.001
nsteps                 = 1000000
init_step              = 0
comm-mode                = Linear
nstcomm                  = 1
comm-grps                =
bd-fric                  = 0
ld-seed                  = 1993
emtol                    = 1000.0
emstep                   = 0.001
niter                    = 20
fcstep                   = 0
nstcgsteep               = 1000
nbfgscorr                = 10
nstxout                  = 1000
nstvout                  = 2000
nstfout                  = 2000
nstcheckpoint            = 10000
nstlog                   = 100
nstenergy                = 1000
nstxtcout                = 1000
xtc-precision            = 1000
xtc-grps                 = protein ;SOL UNK CL-
energygrps               = protein ;SOL UNK CL-
nstlist                  = 10
ns_type                  = Grid
pbc                      = xyz
rlist                    = 0.9
domain-decomposition     = no
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 0.9
epsilon_r                = 1
epsilon_rf               = 1
vdw-type                 = Cut-off
rvdw-switch              = 0
rvdw                     = 1.4
DispCorr                 = EnerPres
table-extension          = 1
energygrp_table          =
fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order                = 4
ewald_rtol               = 1e-5
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = yes
gb_algorithm             = Still
nstgbradii               = 1
rgbradii                 = 2
gb_saltconc              = 0
implicit_solvent         = No
tcoupl                   = berendsen
tc-grps                  = protein  ; sol   CL-  UNK
tau_t                    = 0.1      ; 0.1   0.1  0.1
ref_t                    = 298        ; 298   298  298
Pcoupl                   = no
Pcoupltype               = Isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0       1.0   1.0
andersen_seed            = 815131

gen-vel                  = no
gen-temp                 = 298
gen-seed                 = 173529
constraints              = all-bonds
constraint-algorithm     = Shake
unconstrained-start      = yes
Shake-SOR                = no
shake-tol                = 1e-04
lincs-order              = 4
lincs-iter               = 2
lincs-warnangle          = 60
morse                    = no
energygrp_excl           =
disre                    = No
disre-weighting          = Conservative
disre-mixed              = no
disre-fc                 = 1000
disre-tau                = 0
nstdisreout              = 100
orire                    = no
orire-fc                 = 0
orire-tau                = 0
orire-fitgrp             =
nstorireout              = 100
dihre                    = No
dihre-fc                 = 1000
dihre-tau                = 0
nstdihreout              = 100

free-energy              = no
init-lambda              = 0
delta-lambda             = 0
sc-alpha                 = 0
sc-power                 = 0
sc-sigma                 = 0.3

Stanislav Bobritsky,
ChemBio Center, Taras Shevchenko National University, Kiev, Ukraine.
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