[gmx-users] position restrains while pull simulation

[Justin Lemkul]

On 9/27/14 3:24 PM, shivangi nangia wrote:
> Thanks for the guidance.
>
> Generated posre.itp for popc and cardiolipin for their respective single
> molecules.
> grompp did not give error.
> However, after the pull simulation now, the Protein did not get pull.
> COM of Protein before and after 400th configuration gives the same COM.
>
>
> My topology file:
>
> #include "martini_v2.P.itp"
> #include "martini_v2.0_lipids.itp"
> #ifdef POSRES
> #include "posre_popc.itp"
> #endif
> #include "Protein_X.itp"
> #include "cardio-1.itp"
> #ifdef POSRES
> #include "posre_card.itp"
> #endif
> #include "martini_v2.0_ions.itp"
> #define RUBBER_BANDS
>
>
> [ system ]
> ; name
> Martini system from model.1.pdb
>
> [ molecules ]
> ; name        number
> Protein_X   1
> POPC        230
> CL4         58
> PW          15984
> NA+              273
> CL-              208
>
> ___________________________________________________________________________________________
>
>
> Details of .mdp file:
> define = -DPOSRES
> ;
> ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.1
> ;
> ; for use with GROMACS 4
> ;
>
> ; RUN CONTROL PARAMETERS
> ; MARTINI - Most simulations are stable with dt=40 fs, some (especially
> rings)
> ; require 20-30 fs.
> ; The range of time steps used for parametrization is 20-40 fs, using
> smaller
> ; time steps is therefore not recommended.
> integrator               = md
> ; Start time and timestep in ps:
> tinit                    = 0.0
> dt                       = 0.020
> nsteps                   = 20000 ; 4 ns
> ; Number of steps for center of mass motion removal:
> nstcomm                  = 10
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f):
> nstxout                  = 5000
> nstvout                  = 5000
> nstfout                  = 5000
> ; Output frequency for energies to log (.log) file and energy (.edr) file:
> nstlog                   = 1000
> nstenergy                = 1000
> ; Output frequency and precision for .xtc file:
> nstxtcout                = 50
> xtc_precision            = 100
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; MARTINI - No need for more frequent updates or larger neighborlist cut-off
> ; due to the use of shifted potential energy functions.
> ; Neighborlist update frequency:
> nstlist                  = 10
> ; Neighbor searching algorithm (simple|grid):
> ns_type                  = grid
> ; Periodic boundary conditions (xyz|none):
> pbc                      = xyz
> ; Neighborlist cut-off:
> rlist                    = 1.4
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; MARTINI - VdW and electrostatic interactions are used in their shifted
> forms.
> ; Changing to other types of electrostatics will affect the general
> performance
> ; of the model.
> ; Method for doing electrostatics:
> coulombtype              = Shift
> rcoulomb_switch          = 0.0
> rcoulomb                 = 1.2
> ; Dielectric constant (DC) for cut-off or DC of reaction field:
> epsilon_r                = 2.5
> ; Method for doing Van der Waals:
> vdw_type                 = Shift
> ; Cut-off lengths:
> rvdw_switch              = 0.9
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure?
> DispCorr                 = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; MARTINI -Normal temperature and pressure coupling schemes can be used. It
> ; is recommended to couple individual groups in your system seperately.
> ; Temperature coupling:
> tcoupl                   = berendsen
> ; Groups to couple separately:
> tc-grps                  = Protein W_ION Lipid
> ; Time constant (ps) and reference temperature (K):
> tau_t                    = 1.0 1.0 1.0
> ref_t                    = 323 323 323
> ; Pressure coupling:
> Pcoupl                   = berendsen
> Pcoupltype               = semiisotropic
> refcoord_scaling         = com
> ; Time constant (ps), compressibility (1/bar) and reference P (bar):
> tau_p                    = 3.0 3.0
> compressibility          = 3e-5 3e-5
> ref_p                    = 1.0 1.0
>
> ; GENERATE VELOCITIES FOR STARTUP RUN:
> gen_vel                  = yes
> gen_temp                 = 323
> gen_seed                 = -1
>
> ; OPTIONS FOR BONDS
> ; MARTINI - For ring systems constraints are defined which are best handled
> ; using Lincs.
> constraints              = none
> ; Type of constraint algorithm:
> constraint_algorithm     = Lincs
> ; Do not constrain the start configuration:
> unconstrained_start      = no
> ; Highest order in the expansion of the constraint coupling matrix:
> lincs_order              = 4
> ; Lincs will write a warning to the stderr if in one step a bond rotates
> over
> ; more degrees than:
> lincs_warnangle          = 90
>
> pull            = umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim        = N N Y
> pull_vec1       = 0 0 -1    ; pull direction
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Lipid ;stays still
> pull_group1     = Protein ; moves
> pull_init1      = 0
> pull_rate1      = 0.01       ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>
> _________________________________________________________________________________________________________
>
> I have an index file with groups: Protein, popc + cardiolipin combined as
> Lipid and water + ions as W_ION
>
> grompp_mpi -f my_genconf_pull.mdp -c 1shortmd.gro -n 1indexsys.ndx -p
> my_pull.top -o my_genconf_pull.tpr -maxwarn 1
>
> Before the restraint problem, POPC and cardiolipin were getting drained
> alongwith Protein, but now they are restrained how I want but but Protein
> isnt moving.
>

Is there an #ifdef POSRES block in protein_X.itp?  If so, you're simply 
restraining everything unintentionally.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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