[gmx-users] position restrains while pull simulation
shivangi nangia
shivangi.nangia at gmail.com
Sat Sep 27 21:24:52 CEST 2014
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.
Kindly excuse for the detailed e-mail, not sure where I am going wrong now.
Thanks,
sxn
On Sat, Sep 27, 2014 at 1:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/27/14 12:39 PM, shivangi nangia wrote:
>
>> Thanks Tsjerk and Justin.
>>
>> I have a follow up question.
>>
>> To generate separate restraint .itp file for popc and cardiolipin.
>>
>> genrestr_mpi -f 1shortmd.gro -o posre_card.itp -n 1indexsys.ndx
>> genrestr_mpi -f 1shortmd.gro -o posre_popc.itp -n 1indexsys.ndx
>>
>> Then, I tried 2 approaches:
>>
>> A) Include the separate posre_popc.itp and posre_card.itp at the end of
>> the
>> respective .itp files as:
>> #ifdef POSRES
>> #include "posre_card.itp"
>> #endif
>>
>> #ifdef POSRES
>> #include "posre_popc.itp"
>> #endif
>>
>> And, included define = -DPOSRES in the .mdp file.
>>
>>
>>
>> B) To include individual restraint files in the top file, as suggested by
>> Justin in the link:
>> http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_
>> restraints_out_of_bounds
>>
>> #include "martini_v2.P.itp"
>> #include "my_martini_v2.0_lipids.itp"
>> #ifdef POSRES
>> #include "posre_popc.itp"
>> #endif
>> #include "Protein_X.itp"
>> #include "my_cardio-1.itp"
>> #ifdef POSRES
>> #include "posre_card.itp"
>> #endif
>> #include "martini_v2.0_ions.itp"
>> #define RUBBER_BANDS
>>
>> And, included define = -DPOSRES in the .mdp file
>>
>>
>>
>> I get error in both the approaches.
>>
>>
> Well, what's the error? The "out of bounds" error? As the help text in
> genrestr tells you, "genrestr will only produce a useful file for the first
> molecule," so if you're trying to process multiple molecules at any point,
> it will fail. Generate a posre.itp file from a coordinate file of a single
> molecule, one that is numbered from 1 and does not use global atom
> numbering.
>
> -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
>
> ==================================================
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