[gmx-users] Re: gmx-users Digest, Vol 71, Issue 37
sunita gupta
sunita.bio at gmail.com
Wed Mar 10 11:12:19 CET 2010
Thanks Justin
After going through the discussion on mailing list I got to know that
"coulombic and LJ interections has to be decoupled separately and for better
scaling Lambda should have closer values. But my query is that for what
value of lambda LJ has to be decoupled and for values of lambda coulombic
interactions has to be decoupled.
Like if I am having 11 lambda values ranging from 0 to 1...with successive
increase of 0.1, what range of of lambda should have
couple-lambda0 = vdw-q
couple-lambda1 = vdw
(...to decouple only Coulombic interactions)
and what lambda values should have
couple-lambda0 = vdw
couple-lambda1 = none
(...to decouple van der Waals)
And what should be the value of couple-intramol:
Thanks in Advance
On Sun, Mar 7, 2010 at 10:55 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Calculating Binding Affinity between Protein and Ligand using
> FEP (sunita gupta)
> 2. Re: Calculating Binding Affinity between Protein and Ligand
> using FEP (Justin A. Lemkul)
> 3. SV: [gmx-users] Order parameter for unsaturated lipid chain
> in UAmodel (Tim Sirk)
> 4. Force between groups (Michael McGovern)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 6 Mar 2010 19:30:33 +0530
> From: sunita gupta <sunita.bio at gmail.com>
> Subject: [gmx-users] Calculating Binding Affinity between Protein and
> Ligand using FEP
> To: gmx-users at gromacs.org
> Message-ID:
> <2f68b8d51003060600l58cdb4ecoff09d97b667458c at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello all
>
> Earlier also I posted a query regarding FEP for protein ligand complex, but
> I dint not help much.
> Again I would like to share detailed information regarding the protocol I
> am
> following for calculation the binding free energy between protein and
> ligand
> using FEP(free energy perturbation) method. Please correct me if I am wrong
> anywhere....as the values of *dVpot/dlambda dEkin/dlambda dG/dl constr
> *are
> continuously coming zero(0).
>
> I followed the gromacs tutorial of protien-ligand complex (
> http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf<http://cinjweb.umdnj.edu/%7Ekerrigje/pdf_files/trp_drug_tutor.pdf>)
> for
> preparing the coordinate and topology file for the whole system.
> For Free energy Calculation I followed the tutorial (
> http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial)
> for lambda value ranging from zero(0) to 1 and setup 11 independent job for
> each lambda value for 5 ns.
> But the* dVpot/dlambda dEkin/dlambda dG/dl constr* values in the *.log
> are
> continuously coming zero.
> Any help will be highly appreciated.
>
> For convenience I am also pasting my pro_constV.mdp (please let me know if
> any parameter is wrong of missing...which is leading to such problem)
>
> ; RUN CONTROL PARAMETERS =
> integrator = md
> ; start time and timestep in ps =
> tinit = 0
> dt = 0.002
> nsteps = 5000000
> ; number of steps for center of mass motion removal =
> nstcomm = 100
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout = 50000
> nstvout = 50000
> nstfout = 0
> ; Output frequency for energies to log file and energy file =
> nstlog = 500
> nstenergy = 500
> energygrps = protein non-protein
> ; Output frequency and precision for xtc file =
> nstxtcout = 5000
> xtc-precision = 1000
> ; This selects the subset of atoms for the xtc file. You can =
> ; select multiple groups. By default all atoms will be written. =
> ;xtc_grps =
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist = 10
> ; ns algorithm (simple or grid) =
> ns_type = grid
> ; Periodic boundary conditions: xyz or none =
> ;pbc = xyz
> ; nblist cut-off =
> rlist = 1.0
> ;domain-decomposition = no
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; Method for doing electrostatics =
> coulombtype = pme
> ;rcoulomb-switch = 0
> rcoulomb = 1.0
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon-r = 1
> ; Method for doing Van der Waals =
> vdw-type = cut-off
> ; cut-off lengths =
> ;rvdw-switch = 0.8
> rvdw = 1.4
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr = EnerPres
> ; Spacing for the PME/PPPM FFT grid =
> fourierspacing = 0.1
> ; FFT grid size, when a value is 0 fourierspacing will be used =
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters =
> pme_order = 6
> ewald_rtol = 1e-06
> epsilon_surface = 0
> optimize_fft = yes
> ;restraints
> ;dihre=yes
> ;dihre-fc=1
> ;nstdihreout=1000
> ;disre=simple
> ;disre_fc=1
> ; Berendsen temperature coupling is on
> Tcoupl = berendsen
> tau_t = 0.1 0.1
> tc_grps = protein non-protein
> ref_t = 300 300
> ;OPTIONS FOR PRESSURE COUPLING
> Pcoupl = berendsen
> tau_p = 0.5
> compressibility = 4.5e-05
> ref_p = 1.0
> ; Free energy control stuff
> free_energy = yes
> init_lambda = 0.0
> delta_lambda = 0
> sc_alpha = 0.5
> sc-power = 1.0
> sc-sigma = 0.3
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel = yes
> gen_temp = 300
> gen_seed = 173529
> ; OPTIONS FOR BONDS =
> constraints = hbonds
> ; Type of constraint algorithm =
> constraint-algorithm = Lincs
> ; Do not constrain the start configuration =
> unconstrained-start = no
> ; Relative tolerance of shake =
> shake-tol = 0.0001
> ; Highest order in the expansion of the constraint coupling matrix =
> lincs-order = 12
> ; Lincs will write a warning to the stderr if in one step a bond =
> ; rotates over more degrees than =
> lincs-warnangle = 30
>
> Message: 2
> Date: Sat, 06 Mar 2010 10:08:01 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Calculating Binding Affinity between Protein
> and Ligand using FEP
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B926FD1.2090509 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> sunita gupta wrote:
> > Hello all
> >
> > Earlier also I posted a query regarding FEP for protein ligand complex,
> > but I dint not help much.
> > Again I would like to share detailed information regarding the protocol
> > I am following for calculation the binding free energy between protein
> > and ligand using FEP(free energy perturbation) method. Please correct me
> > if I am wrong anywhere....as the values of *dVpot/dlambda
> > dEkin/dlambda dG/dl constr *are continuously coming zero(0).
> >
> > I followed the gromacs tutorial of protien-ligand complex
> > (http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf<http://cinjweb.umdnj.edu/%7Ekerrigje/pdf_files/trp_drug_tutor.pdf>)
> for
> > preparing the coordinate and topology file for the whole system.
> > For Free energy Calculation I followed the tutorial
> > (
> http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial)
> > for lambda value ranging from zero(0) to 1 and setup 11 independent job
> > for each lambda value for 5 ns.
> > But the* dVpot/dlambda dEkin/dlambda dG/dl constr* values in the *.log
> > are continuously coming zero.
> > Any help will be highly appreciated.
> >
>
> What version of Gromacs are you using? If it's 3.3.x, you need to define a
> B-state for the molecule that you're trying to decouple. Furthermore, you
> should be decoupling charges and vdW parameters in separate steps; I
> believe
> that is mentioned in the tutorial material you quote above, and if not, it
> has
> surely been posted to this list several times.
>
> If you're using version 4.0.x, note that the free energy options have
> changed
> somewhat. Changes to the topology are not necessary, but different options
> must
> be set in the .mdp file. See the manual.
>
> -Justin
>
> > For convenience I am also pasting my pro_constV.mdp (please let me know
> > if any parameter is wrong of missing...which is leading to such problem)
> >
> > ; RUN CONTROL PARAMETERS =
> > integrator = md
> > ; start time and timestep in ps =
> > tinit = 0
> > dt = 0.002
> > nsteps = 5000000
> > ; number of steps for center of mass motion removal =
> > nstcomm = 100
> > ; OUTPUT CONTROL OPTIONS =
> > ; Output frequency for coords (x), velocities (v) and forces (f) =
> > nstxout = 50000
> > nstvout = 50000
> > nstfout = 0
> > ; Output frequency for energies to log file and energy file =
> > nstlog = 500
> > nstenergy = 500
> > energygrps = protein non-protein
> > ; Output frequency and precision for xtc file =
> > nstxtcout = 5000
> > xtc-precision = 1000
> > ; This selects the subset of atoms for the xtc file. You can =
> > ; select multiple groups. By default all atoms will be written. =
> > ;xtc_grps =
> > ; NEIGHBORSEARCHING PARAMETERS =
> > ; nblist update frequency =
> > nstlist = 10
> > ; ns algorithm (simple or grid) =
> > ns_type = grid
> > ; Periodic boundary conditions: xyz or none =
> > ;pbc = xyz
> > ; nblist cut-off =
> > rlist = 1.0
> > ;domain-decomposition = no
> > ; OPTIONS FOR ELECTROSTATICS AND VDW =
> > ; Method for doing electrostatics =
> > coulombtype = pme
> > ;rcoulomb-switch = 0
> > rcoulomb = 1.0
> > ; Dielectric constant (DC) for cut-off or DC of reaction field =
> > epsilon-r = 1
> > ; Method for doing Van der Waals =
> > vdw-type = cut-off
> > ; cut-off lengths =
> > ;rvdw-switch = 0.8
> > rvdw = 1.4
> > ; Apply long range dispersion corrections for Energy and Pressure =
> > DispCorr = EnerPres
> > ; Spacing for the PME/PPPM FFT grid =
> > fourierspacing = 0.1
> > ; FFT grid size, when a value is 0 fourierspacing will be used =
> > fourier_nx = 0
> > fourier_ny = 0
> > fourier_nz = 0
> > ; EWALD/PME/PPPM parameters =
> > pme_order = 6
> > ewald_rtol = 1e-06
> > epsilon_surface = 0
> > optimize_fft = yes
> > ;restraints
> > ;dihre=yes
> > ;dihre-fc=1
> > ;nstdihreout=1000
> > ;disre=simple
> > ;disre_fc=1
> > ; Berendsen temperature coupling is on
> > Tcoupl = berendsen
> > tau_t = 0.1 0.1
> > tc_grps = protein non-protein
> > ref_t = 300 300
> > ;OPTIONS FOR PRESSURE COUPLING
> > Pcoupl = berendsen
> > tau_p = 0.5
> > compressibility = 4.5e-05
> > ref_p = 1.0
> > ; Free energy control stuff
> > free_energy = yes
> > init_lambda = 0.0
> > delta_lambda = 0
> > sc_alpha = 0.5
> > sc-power = 1.0
> > sc-sigma = 0.3
> > ; GENERATE VELOCITIES FOR STARTUP RUN =
> > gen_vel = yes
> > gen_temp = 300
> > gen_seed = 173529
> > ; OPTIONS FOR BONDS =
> > constraints = hbonds
> > ; Type of constraint algorithm =
> > constraint-algorithm = Lincs
> > ; Do not constrain the start configuration =
> > unconstrained-start = no
> > ; Relative tolerance of shake =
> > shake-tol = 0.0001
> > ; Highest order in the expansion of the constraint coupling matrix =
> > lincs-order = 12
> > ; Lincs will write a warning to the stderr if in one step a bond =
> > ; rotates over more degrees than =
> > lincs-warnangle = 30
> >
> >
> >
> > --
> > Best Regards
> > SUNITA GUPTA
> > Member Research Team
> > LeadInvent Technology
> > TBIU, IIT Delhi, India
> > Email- sunita at leadinvent.com <mailto:sunita at leadinvent.com>
> > Ph- +9111 26581524 (Ex-6)
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 01 Mar 2010 22:04:19 -0500
> From: Tim Sirk <tsirk at vt.edu>
> Subject: SV: [gmx-users] Order parameter for unsaturated lipid chain
> in UAmodel
> To: gmx-users at gromacs.org
> Cc: tsirk at vt.edu
> Message-ID: <1267499059.12129.3.camel at redhacker>
> Content-Type: text/plain; charset="UTF-8"
>
> Sarah,
>
> I remember some changes to the double bond awhile back, perhaps you're
> using those?
>
> POPC (Berger/Tielman) is normally 'smoother' as Justin says. Maybe
> someone has a reference for the updates.
>
>
> Tim Sirk
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 6 Mar 2010 21:24:52 -0800 (PST)
> From: Michael McGovern <mpmcgovern at wisc.edu>
> Subject: [gmx-users] Force between groups
> To: gmx-users at gromacs.org
> Message-ID: <839220.61003.qm at web65701.mail.ac4.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi everyone. I have a trajectory file and for some analysis I'm doing I
> need to calcualte the force between two groups of atoms. Is there way to do
> this? Thank you.
>
>
>
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