Hi, On Tue, Sep 26, 2017 at 3:38 PM Du, Yu <[email protected]> wrote:
> Thank Mark's reply. > > > -----Original Messages----- > > From: "Mark Abraham" <[email protected]> > > Sent Time: 2017-09-26 19:44:41 (Tuesday) > > To: [email protected] > > Cc: > > Subject: Re: [gmx-users] Group NS scheme parameter for 2016.3 version > > > > Hi, > > > > On Tue, Sep 26, 2017 at 4:02 AM Du, Yu <[email protected]> wrote: > > > > > > -----Original Messages----- > > > > From: "Mark Abraham" <[email protected]> > > > > Sent Time: 2017-09-26 06:38:40 (Tuesday) > > > > To: "Discussion list for GROMACS users" <[email protected]>, > > > "Discussion list for GROMACS users" < > > > [email protected]> > > > > Cc: > > > > Subject: Re: [gmx-users] Group NS scheme parameter for 2016.3 version > > > > > > > > Hi, > > > > > > > > On Mon, 25 Sep 2017 14:11 Du, Yu <[email protected]> wrote: > > > > > > > > > Dear GMX Users, > > > > > > > > > > > > > > > Indeed making tabulized potential between groups with Verlet is not > > > > > trivial as also discussed in OpenMM issue #1765. > > > > > > > > > > I'm using gmx 2016.3. If I want use the group NS scheme as precise > as > > > > > possible, what parameters in mdp file should I set and what are > their > > > > > recommended values for protein and ligand system. > > > > > > > > > > > > > It's straightforward to implement a tabulated interaction kernel, but > > > > rather less clear how best to let the user describe to mdrun how they > > > want > > > > the calculation to work, eg whether interaction types should be > governed > > > by > > > > atom numbers, or types, or names, and how that should be expressed > in the > > > > topology. Suggestions for problem types people want to be able to > handle > > > > are most welcome. > > > > > > > > > > I want to decompose the interaction between protein and ligand, and > only > > > between them, not others. > > > So I think "vdwtype=user, energygrps = Protein Ligand, energygrp-table > = > > > Protein Ligand and table.xvg table_Protein_ligand.xvg" is the only > solution > > > in gromacs to achieve it. > > > > > > > Yes. So in future, some method that would select the regions to use the > > different tabulated interactions based on atom number (ie index groups) > > would work for you. > > Today I experimented on the tabulated potential with group cut-off scheme. > I used custom potential (no coulomb and no attractive vdw) between protein > and ligand. I guess it worked. Could you please have a look at the md.log > and md.mdp file? and help me assure that there is no question. > ----------------------md.log----------------------- > Table routines are used for coulomb: true > Table routines are used for vdw: true > Cut-off's: NS: 1 Coulomb: 1 LJ: 1 > Long Range LJ corr.: <C6> 3.4946e-04 > System total charge: -0.000 > Read user tables from md_0_3.xvg with 1001 data points. > Tabscale = 500 points/nm > Read user tables from md_0_3_Protein_MEL.xvg with 1001 data points. > Tabscale = 500 points/nm > Read user tables from md_0_3.xvg with 1001 data points. > Tabscale = 500 points/nm > Read user tables from md_0_3.xvg with 1001 data points. > Tabscale = 500 points/nm > ............................... > Statistics over 100001 steps using 1001 frames > > Energies (kJ/mol) > Bond Angle Proper Dih. Improper Dih. LJ-14 > 4.09718e+03 1.11493e+04 1.26265e+04 8.33816e+02 4.52508e+03 > Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Potential > 4.81316e+04 4.01305e+04 -2.28798e+03 -4.91463e+05 -3.72257e+05 > Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) > 8.98371e+04 -2.82420e+05 2.61416e+06 3.37891e+02 -2.51191e+02 > Pressure (bar) Constr. rmsd > 5.71728e+02 0.00000e+00 > > Total Virial (kJ/mol) > 2.46727e+04 1.69577e+01 5.39006e+01 > 1.69965e+01 2.48000e+04 -4.34063e+01 > 5.38208e+01 -4.28545e+01 2.47416e+04 > > Pressure (bar) > 5.78692e+02 -5.85172e+00 -3.91771e+00 > -5.85597e+00 5.67516e+02 7.54656e+00 > -3.90895e+00 7.48597e+00 5.68976e+02 > > Epot (kJ/mol) Coul-SR LJ-SR Coul-14 LJ-14 > Protein-Protein -8.49851e+04 -8.95750e+03 4.83260e+04 4.44865e+03 > Protein-MEL 0.00000e+00 1.57386e+01 0.00000e+00 0.00000e+00 > Protein-rest -3.16047e+04 -1.50902e+03 0.00000e+00 0.00000e+00 > MEL-MEL -3.28886e+02 -2.02938e+01 -1.94359e+02 7.64322e+01 > MEL-rest -1.16305e+03 -6.90968e+01 0.00000e+00 0.00000e+00 > rest-rest -3.73381e+05 5.06707e+04 0.00000e+00 0.00000e+00 > > T-MEL_NA_Protein T-SOL_CL > 3.41647e+02 3.37007e+02 > ----------------------md.log----------------------- > Seems plausible. > ----------------------md.mdp----------------------- > ; Run parameters > integrator = md-vv > nsteps = 100000 ; 200ps > dt = 0.002 > > ; Output parameters > nstxout = 0 > nstvout = 0 > nstenergy = 500 ; 1ps > nstlog = 500 > nstxout-compressed = 500 > compressed-x-grps = System > energygrps = Protein MEL > energygrp-table = Protein MEL > > ; Neighbor searching > nstlist = 5 ; 10fs > ns-type = Grid > pbc = xyz > rlist = 1.0 > cutoff-scheme = group > nstcalclr = -1 > > ; Electrostatics and VdW > coulombtype = user > rcoulomb = 1.0 > vdwtype = user > rvdw = 1.0 > > ; Temperature coupling > Tcoupl = nose-hoover > tc-grps = MEL_NA_Protein SOL_CL > tau_t = 1.0 1.0 > ref_t = 300 300 > > ; Pressure coupling > Pcoupl = no > ; Dispersion correction > DispCorr = EnerPres > > ; Velocity generation > gen_vel = no > > ; Bond parameters > continuation = yes > constraint-algorithm = lincs > constraints = h-bonds > lincs-order = 6 > lincs-iter = 2 > ----------------------md.mdp----------------------- > > > > > > How to set up the nonbonded scheme for a given force field varies with > the > > > > force field, either based on how it was parameterized or been shown > to > > > work > > > > in practice. This is standard practice. A major defect of the group > > > scheme > > > > is that it is inefficient with a buffered list, but that is your > tradeoff > > > > to make. > > > > > > > > > > Yes, this is my major confusion. Amber FF don't use charge group not > like > > > GROMOS FF. I need to work with Amber FF, so is it proper to use > > > amber99sb-ildn and gaff with group cut-off scheme? > > > > > > > Using charge groups of size 1 is the same as not using charge groups, > which > > is how the AMBER force fields were already implemented, long before the > > Verlet scheme was implemented. You should also be reading other people's > > work that used GROMACS and the AMBER force fields... > > > > Yes, I'm really cramming. > > > > > > And now the manual and user guide is dominated by Verlet cut-off > scheme, > > > where can I find the guide of using group cut-off scheme? I can't tell > > > which options is for group scheme in the Molecular dynamics parameters > > > (.mdp). > > > > > > > Nothing's been removed, and nearly everything works the same way. > > > http://manual.gromacs.org/documentation/2016.4/user-guide/mdp-options.html#neighbor-searching > > and > > the coulomb and vdw sections are the only bits that matter, and they note > > the points of difference. > > > > Thanks for the clue, I'll note that part. > > > > > > The following is what I found in > > > > regressiontests-2016.3/kernel/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4/grompp.mdp > > > ; NEIGHBORSEARCHING PARAMETERS > > > ; cut-off scheme (group: using charge groups, Verlet: particle based > > > cut-offs) > > > cutoff-scheme = Group > > > ; nblist update frequency > > > nstlist = 1 > > > ; ns algorithm (simple or grid) > > > ns-type = Grid > > > ; Periodic boundary conditions: xyz, no, xy > > > pbc = xyz > > > periodic-molecules = no > > > ; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, > > > ; a value of -1 means: use rlist > > > verlet-buffer-drift = 0.005 > > > ; nblist cut-off > > > rlist = 0.99 > > > nstcalclr = -1 > > > > > > > > > Although it use group cut-off scheme, there is also a > verlet-buffer-drift, > > > which doesn't show in the 2016.3 version .mdp option. > > > > > > > Don't use a test input for designing a real simulation. Those are > designed > > to do very specific things, including hit corner cases that we think > nobody > > should use. And that parameter is an old name that is not a problem when > > the group scheme is chosen. > > Of course, I won't use the test .mdp file for real simulation. I use it > for learning operational options, which I also found in older version > Gromacs manual. Thanks for Gromacs' good archive. :) > > > > > You should find some literature that shows the force field and software > > working together, and test it yourself also. Unfortunately I know of > nobody > > who's stepped up and published "this is how you should run *these kinds* > of > > simulations" for AMBER ff in GROMACS. > > Yeah, this part is definitely my job. Thanks for your points. > > > > > So, lots of thanks for anyone's advice for setting group scheme. > > > > > > > Given that you are modifying the force field to add different > > > interactions, > > > > you will anyway have to show that the modified form of the force > field > > > > works suitably. Even if the Verlet scheme had support for tabulated > > > > interactions, you would still be limited to having only one set of > > > > nonbonded parameters per atom type. Is your mix of interaction types > > > > feasible to use with such a restriction? > > > > > > > > > > I'm really looking forward to the combination of Verlet cut-off scheme > > > with the tabulated potential. :) > > > > > > > That wasn't the question. Can your ligand atoms have *one* set of vdw > > parameters that can interact with solvent, ligand and protein atoms > > according to different functional forms? People sometimes ask for such > > Only the protein and ligand interaction is under the effect of tabulated > potential. If I fully understand the Tabulated potential tutorial, what I > set doesn't affact the normal interaction between other groups. > Yes. But the shape of the interaction is only one of the relevant things. The parameters, which scale the shape, are another. You have to have the same *values*. Maybe that's for free with WCA, but it wouldn't be with say Buckingham. There you would have to do something creative with scaling of the shape. Mark > > things without thinking through whether their model makes sense (and if > it > > does, whether they would require schizophrenic atoms). > > Turning off the specific interaction between protein and ligand not other > groups. I think this is really what a crazy me need. :) > > Yu > > > > > Mark > > > > > Mark > > > > > > > > > > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > send a mail to [email protected]. > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to [email protected]. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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