[gmx-users] How to fix molecules in gromacs?

[Justin Lemkul]

On 7/16/16 8:35 AM, Daniele Veclani wrote:
> Dear gromacs users.
>
> I'm trying to fix a molecule inside the box. I want to use this molecule as
> an immobile reference in the pulling simulations.
>
> I can i do this? I have to use the position restraint or freezing Group?
>
> I tried to use position restraint, but, by analyzing the trajectories,
> I see that
> the molecule out of the box.
>
> This is my .top file:
> -----------------------------------
> ; Topology of CNT and CFX
> ;-----------------------------------
> #include "gromos54a7_atb.ff/forcefield.itp"
>
> ;-----------------------------------------------
> ; Uncomment the line with needed topology below
> ;-----------------------------------------------
> ; #include "zw"
>
> #include "cipro.itp"
>
> ; #include cnt
>
> #include "nano.itp"
> #ifdef DPOSRES_0PCZ
> #include "cnt-posre.itp"
> #endif
>
> #include "gromos54a7_atb.ff/spce.itp"
>
> [ system ]
> cnt-cipro
> [ molecules ]
> ; Compound        nmols
> AUT8             1
> 0PCZ             1
> SOL              39030
>
> This is may .mdp file:
>
> ;preprocessing
> define                   = -DPOSRES_0PCZ

Your syntax is wrong.  The "-D" prefix needs to be added to whatever the #ifdef 
keyword is.  So for your topology to work, you need "define = -DDPOSRES_0PCZ"

Or, you can use -DPOSRES_0PCZ with #ifdef POSRES_0PCZ.

You can check that no restraints are functioning by looking in the .log file, as 
you will find no "Position Rest." energy term.  If the restraints are active, 
the associated energy is written.

-Justin

> ; Run control
> integrator               = sd       ; Langevin dynamics
> dt                       = 0.002
> nsteps                   = 300000    ; 0.6 ns
> nstcomm                  = 10
> ; Output control
> nstxout                  = 5000
> nstvout                  = 5000
> nstfout                  = 5000
> nstlog                   = 5000
> nstenergy                = 5000
> nstxout-compressed       = 5000
> ; Neighborsearching and short-range nonbonded interactions
> cutoff-scheme            = verlet
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 0.8
> ; Electrostatics
> coulombtype              = PME
> rcoulomb                 = 1.2
> ; van der Waals
> vdwtype                  = cutoff
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                  = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
> ; Temperature coupling
> ; tcoupl is implicitly handled by the sd integrator
> tcoupl                   = Nose-Hoover
> tc_grps                  = system
> tau_t                    = 1.0
> ref_t                    = 298.15
> ; Pressure coupling is on for pull
> Pcoupl                   = Parrinello-Rahman
> tau_p                    = 0.5
> compressibility          = 4.5e-05
> ref_p                    = 1.0
> ; Free energy control stuff
> ; Generate velocities to start
> gen_vel                  = no
> gen_temp                 = 298.15
> gen_seed                 = -1
> ; options for bonds
> constraints              = h-bonds  ; we only have C-H bonds here
> ; Type of constraint algorithm
> constraint-algorithm     = lincs
> ; Do not constrain the starting configuration
> continuation             = yes
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order              = 4
> lincs-iter               = 1
> ; Pull code
> pull                    = umbrella
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_group1_name        = AUT8
> pull_group2_name        = 0PCZ
> pullgeometry            = distance      ; simple distance increase
> pull_coord1_groups = 1 2
> pull_dim                = N Y N
> pull_coord1_rate        = 0.01          ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
> pull_start              = yes
>
> How can I fix this problem??
>
> I use gromacs 5.0.4
>
> Best regards
> D.V.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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