[gmx-users] NMR restrained MD
Rama Krishna Koppisetti
ramkishna72 at gmail.com
Fri Sep 6 23:35:42 CEST 2013
H
i Justin,
Thanks for your reply.
How to do that?
On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/6/13 5:23 PM, Rama wrote:
>
>> Hi,
>>
>> I'm doing NMR restrained MD simulation for protein-Bilayer system to
>> satisfy
>> NMR experimental data.
>>
>> Without restraints there is no problem, but if I include distance
>> restraints
>> in topology file, getting fatal error:
>>
>> the lipid atom index # was not recognized by using this command:
>> g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
>> md.tpr -maxwarn 5
>>
>> even in index file protein_DMPC atoms index is there continuously. Any one
>> have suggestions to overcome this fatal error. Thanks
>>
>> /
>> [ file beta_disres.itp, line 4 ]:
>> Atom index (2679) in distance_restraints out of bounds (1-2513)./
>>
>>
> Just like position restraints, distance restraints only work within a
> [moleculetype]. Thus you're probably trying to restrain atoms between
> [moleculetype] directives, which does not work. You could theoretically
> make a merged [moleculetype] of whatever species need to be restrained, but
> that may take a bit of effort depending on what is being restrained.
>
> -Justin
>
>
> md.mdp file:
>> title = protein-bilayer complex
>> define = -DDISRES ; NMR Distance restraints
>> ; Run parameters
>> integrator = md ; leap-frog integrator
>> nsteps = 2500000 ;
>> dt = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 5000 ; save coordinates every 5 ps
>> nstvout = 5000 ; save velocities every 5 ps
>> nstxtcout = 5000 ; xtc compressed trajectory output every
>> 5 ps
>> nstenergy = 5000 ; save energies every 5 ps
>> nstlog = 5000 ; update log file every 5 ps
>> ; Bond parameters
>> continuation = yes ; Restarting after NPT
>> constraint_algorithm = lincs ; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H
>> bonds)
>> constrained
>> lincs_iter = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>> ; Distance restraints parameters
>> disre = simple ; simple (per-molecule)
>> disre_fc = 1000 ; force constant for distance restraints
>> ; Neighborsearching
>> ns_type = grid ; search neighboring grid cels
>> nstlist = 5 ; 10 fs
>> rlist = 1.2 ; short-range neighborlist cutoff (in nm)
>> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
>> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype = PME ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order = 4 ; cubic interpolation
>> fourierspacing = 0.16 ; grid spacing for FFT
>> ; Temperature coupling is on
>> tcoupl = Nose-Hoover ; More accurate thermostat
>> tc-grps = Protein non-protein non-protein ; three
>> coupling groups -
>> more accurate
>> tau_t = 0.5 0.5 0.5 ; time constant,
>> in ps
>> ref_t = 303 303 303 ; reference
>> temperature, one for
>> each group, in K
>> ; Pressure coupling is on
>> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
>> pcoupltype = semiisotropic ; uniform scaling of x-y box
>> vectors,
>> independent z
>> tau_p = 2.0 ; time constant, in ps
>> ref_p = 1.0 1.0 ; reference pressure,
>> x-y, z (in bar)
>> compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility,
>> bar^-1
>> ; Periodic boundary conditions
>> pbc = xyz ; 3-D PBC
>> ; Dispersion correction
>> DispCorr = EnerPres ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = no ; Velocity generation is off
>> ; COM motion removal
>> ; These options remove motion of the protein/bilayer relative to the
>> solvent/ions
>> nstcomm = 1
>> comm-mode = Linear
>> comm-grps = protein non-protein
>>
>> topology file:
>>
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> ; Include Distance restraints file
>> #ifdef DISRES
>> #include "beta_disres.itp"
>> #endif
>>
>> ; Strong position restraints for InflateGRO
>> #ifdef STRONG_POSRES
>> #include "strong_posre.itp"
>> #endif
>>
>> ; Include DMPC topology
>> #include "ramaLJ.ff/dmpcLJ.itp"
>>
>> ; Include water topology
>> #include "ramaLJ.ff/spc.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ; i funct fcx fcy fcz
>> 1 1 1000 1000 1000
>> #endif
>>
>> ; Include topology for ions
>> #include "ramaLJ.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Giving Russians Opium May Alter Current Situation in water
>>
>> [ molecules ]
>> ; Compound #mols
>> Protein 1
>> DMPC 125
>> SOL 8335
>> CL 8
>>
>>
>>
>> --
>> View this message in context: http://gromacs.5086.x6.nabble.**
>> com/NMR-restrained-MD-**tp5011025.html<http://gromacs.5086.x6.nabble.com/NMR-restrained-MD-tp5011025.html>
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>
>>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
>
> --
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