[gmx-users] DNA-protein complex
Justin Lemkul
jalemkul at vt.edu
Wed Mar 18 12:43:25 CET 2015
On 3/18/15 4:26 AM, Urszula Uciechowska wrote:
>
> The force field that I used was ambe99bsc0, and my input file was:
What is the DNA sequence? We have seen some cases where AMBER99-parmbsc0 fails
to capture global characteristics of DNA structure. This is a common problem
among additive nucleic acid force fields. In general, AMBER and CHARMM
parameter sets are quite good, but there are times when they can fail. See, for
instance, a comparison including this AMBER parameter set in
http://dx.doi.org/10.1021/jz5024543
-Justin
> ; 7.3.3 Run Control
> integrator = md ; md integrator
> tinit = 0 ; [ps] starting time for run
> dt = 0.002 ; [ps] time step for
> integration
> nsteps = 5000000 ; maximum number of steps
> to integrate, 0.002 * 2,500,000 = 5,000 ps
> comm_mode = Linear ; remove center of mass
> translation
> nstcomm = 1 ; [steps] frequency of
> mass motion removal
> comm_grps = Protein Non-Protein ; group(s) for center of
> mass motion removal
>
> ; 7.3.8 Output Control
> nstxout = 2500000 ; [steps] freq to write
> coordinates to trajectory
> nstvout = 2500000 ; [steps] freq to write velocities
> to trajectory
> nstfout = 2500000 ; [steps] freq to write forces to
> trajectory
> nstlog = 100 ; [steps] freq to write energies
> to log file
> nstenergy = 500 ; [steps] freq to write energies
> to energy file
> nstxtcout = 500 ; [steps] freq to write
> coordinates to xtc trajectory
> xtc_precision = 1000 ; [real] precision to write xtc
> trajectory
> xtc_grps = System ; group(s) to write to xtc trajectory
> energygrps = System ; group(s) to write to energy file
>
> ; 7.3.9 Neighbor Searching
> nstlist = 1 ; [steps] freq to update neighbor
> list
> ns_type = grid ; method of updating neighbor list
> pbc = xyz ; periodic boundary conditions in
> all directions
> rlist = 0.8 ; [nm] cut-off distance for the
> short-range neighbor list
>
> ; 7.3.10 Electrostatics
> coulombtype = PME ; Particle-Mesh Ewald electrostatics
> rcoulomb = 0.8 ; [nm] distance for Coulomb cut-off
>
> ; 7.3.11 VdW
> vdwtype = cut-off ; twin-range cut-off with rlist
> where rvdw >= rlist
> rvdw = 0.8 ; [nm] distance for LJ cut-off
> DispCorr = EnerPres ; apply long range dispersion
> corrections for energy
>
> ; 7.3.13 Ewald
> fourierspacing = 0.12 ; [nm] grid spacing for FFT grid
> when using PME
> pme_order = 4 ; interpolation order for PME, 4 =
> cubic
> ewald_rtol = 1e-5 ; relative strength of
> Ewald-shifted potential at rcoulomb
>
> ; 7.3.14 Temperature Coupling
> tcoupl = v-rescale ; temperature
> coupling with Nose-Hoover ensemble
> tc_grps = Protein Non-Protein ; groups to couple
> seperately to temperature bath
> tau_t = 0.1 0.1 ; [ps] time
> constant for coupling
> ref_t = 310 310 ; [K] reference
> temperature for coupling
>
> ; 7.3.15 Pressure Coupling
> pcoupl = parrinello-rahman ; pressure coupling where
> box vectors are variable
> pcoupltype = isotropic ; pressure coupling in
> x-y-z directions
> tau_p = 2.0 ; [ps] time constant for
> coupling
> compressibility = 4.5e-5 ; [bar^-1] compressibility
> ref_p = 1.0 ; [bar] reference pressure
> for coupling
>
> ; 7.3.17 Velocity Generation
> gen_vel = no ; velocity generation turned off
> ; 7.3.18 Bonds
> constraints = all-bonds ; convert all bonds to constraints
> constraint_algorithm = LINCS ; LINear Constraint Solver
> continuation = yes ; apply constraints to the start
> configuration
> lincs_order = 4 ; highest order in the expansion
> of the contraint coupling matrix
> lincs_iter = 1 ; number of iterations to correct
> for rotational lengthening
> lincs_warnangle = 30 ; [degrees] maximum angle that a
> bond can rotate before LINCS will complain
>
> best regards
> Urszula Uciechowska
>
>
>
>
>> 2015-03-17 14:35 GMT-03:00 Urszula Uciechowska <
>> urszula.uciechowska at biotech.ug.edu.pl>:
>>
>>>
>>>
>>> Hi,
>>>
>>> I am running MD for dsDNA-protein complex. After 50ns I observed that
>>> the
>>> DNA is unwinding. What did go wrong? Should I have changed something in
>>> my
>>> input file?
>>>
>>> You might want to send your input files, so as your force field that you
>> have choose. It is hard to say anything without more details.
>> Also, what do you mean by 'unwinding'? Could you be more specific?
>>
>>
>>> Thank you in advance for your suggestions.
>>> best regards
>>> Urszula
>>>
>>
>> Cheers!
>> --
>> Marcelo Depólo Polêto
>> B.Sc. Biochemistry - University of Viçosa (Brazil)
>> --
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>
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
--
==================================================
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
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