[gmx-users] position restrains while pull simulation
shivangi.nangia at gmail.com
Sat Sep 27 23:09:15 CEST 2014
Yes, there was a #ifdef POSRE block in Protein_X.itp, that I was unaware of.
On Sat, Sep 27, 2014 at 4:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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"
>> #include "Protein_X.itp"
>> #include "cardio-1.itp"
>> #ifdef POSRES
>> #include "posre_card.itp"
>> #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
>> ; require 20-30 fs.
>> ; The range of time steps used for parametrization is 20-40 fs, using
>> ; 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
>> ; 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
>> ; Changing to other types of electrostatics will affect the general
>> ; 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.
>> ; 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
>> ; 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
>> ; 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 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
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