[gmx-users] Charge grps and cut-off

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 17 13:41:13 CEST 2010



Sai Pooja wrote:
> Thanks Justin. How about note 3?
> 
> The largest charge group contains 12 atoms.
>   Since atoms only see each other when the centers of geometry of the charge
>   groups they belong to are within the cut-off distance, too large charge
>   groups can lead to serious cut-off artifacts.
>   For efficiency and accuracy, charge group should consist of a few atoms.
>   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
> 
> This note reappears no matter what the parameter file has. Does this 
> mean I need to make changes in my top file or define charge groups?
> 

Yes, something is wrong with the topology.  You have a charge group that is 
likely unacceptably large.

-Justin

> Pooja
> 
> 
> On Sat, Jul 17, 2010 at 7:25 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Sai Pooja wrote:
> 
>         Hi,
> 
>         This is the .mdp file that produces notes-3 and 4. However, the
>         previous md file produces note-3.
> 
>         ; RUN CONTROL PARAMETERS
>         integrator               = md
>         dt                       = 0.002
>         nsteps                   = 5000000
> 
>         ; OUTPUT CONTROL OPTIONS
>         nstxout                  = 0                    ; No output,
>         except for last frame (coordinates)
>         nstvout                  = 0                    ; No output,
>         except for last frame (velocities)
>         nstfout                  = 0                    ; No output,
>         except for last frame (forces)
>         nstlog                   = 500000                ; Write every
>         step to the log
>         nstenergy                = 500000                    ; Write
>         energies at every step
>         xtc_grps                 = Protein
>         nstxtcout                = 500000                    ; Do not
>         write a compressed trajectory
>         energygrps               = Protein Non-Protein  ; Write energy
>         information separately for these groups
> 
>         ; NEIGHBORSEARCHING PARAMETERS
>         nstlist                  = 5
>         ns-type                  = Grid
>         pbc                      = xyz
>         rlist                    = 2.0
> 
>         ; OPTIONS FOR ELECTROSTATICS AND VDW
>         coulombtype              = Reaction-field-zero
>         rcoulomb                 = 1.8
>         epsilon_rf               = 0
>         vdw-type                 = Switch
>         rvdw                     = 2.0
>         rvdw-switch              = 1.6
> 
> 
>     Well, here's the problem.  Read about proper usage of the switch
>     function, especially the note about the size of rlist:
> 
>     http://manual.gromacs.org/current/online/mdp_opt.html#vdw
> 
>     -Justin
> 
>         ; Spacing for the PME/PPPM FFT
>         fourierspacing           = 0.12
>         ; 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                = 4
>         ewald_rtol               = 1e-05
>         epsilon_surface          = 0
>         optimize_fft             = no
>         ; Temperature coupling
>         tcoupl                   = nose-hoover
>         tc-grps                  = Protein  Non-Protein
>         tau_t                    = 0.2      0.2
>         ref_t                    = 300      300
> 
>         ; Pressure coupling     pcoupl                   = no
> 
>         ; OPTIONS FOR BONDS   constraints              = all-bonds
>          constraint-algorithm     = SHAKE
>         shake_tol                = 0.0001
> 
>         Pooja
> 
> 
> 
>         On Fri, Jul 16, 2010 at 8:51 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            Sai Pooja wrote:
> 
>                Hi,
> 
>                I am trying to reproduce results from a paper which uses this
>                cutoff. The work is on loop-folding and they use implicit
>                solvent. I am using explicit solvent with charmm 27.
>         Below is my
>                mdp file. I am not sure if there is any advantage in using a
>                large cut-off.
> 
> 
> 
>            Large cutoffs can cause artifacts.  This .mdp file also does not
>            match the error message you quoted before.  If it is indeed
>            accurate, then it looks like your .mdp file is being interpreted
>            incorrectly (2.0-nm cutoffs instead of 1.8 nm). If there is a
>            misinterpretation, file a bugzilla.  If you've simply posted the
>            wrong file, please post the correct file, if necessary.  But I'd
>            suggest you do some homework about the effects of long cutoffs,
>            especially if they deviate from what the force field derivation
>            requires.
> 
>            -Justin
> 
>                ; VARIOUS PREPROCESSING OPTIONS
>                title                    = NVT simulation (constant number,
>                pressure and temperature)
>                cpp                      = /lib/cpp
>                define                   =-DPOSRES
> 
>                ; RUN CONTROL PARAMETERS
>                integrator               = md
>                dt                       = 0.002
>                nsteps                   = 100000
> 
>                ; OUTPUT CONTROL OPTIONS
>                nstxout                  = 10000
>                nstvout                  = 0
>                nstfout                  = 0
>                nstlog                   = 10000
>                nstenergy                = 10000
>                nstxtcout                = 0
>                xtc_precision            = 0
>                xtc-grps                 = System
>                energygrps               = Protein Non-Protein
> 
>                ; NEIGHBORSEARCHING PARAMETERS
>                nstlist                  = 5
>                ns-type                  = Grid
>                pbc                      = xyz
>                rlist                    = 1.8
> 
>                ; OPTIONS FOR ELECTROSTATICS AND VDW
>                coulombtype              = PME
>                fourierspacing           = 0.12
>                rcoulomb                 = 1.8
>                epsilon_rf               = 78
>                vdw-type                 = Cut-off
>                rvdw                     = 1.8
> 
>                ; 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                = 4
>                ewald_rtol               = 1e-05
>                epsilon_surface          = 0
>                optimize_fft             = no
> 
>                ; Temperature coupling  Tcoupl                   = Berendsen
>                tc-grps                  = Protein  Non-Protein
>                tau_t                    = 0.2      0.2
>                ref_t                    = 300      300
> 
>                ; Pressure coupling     Pcoupl                   = Berendsen
>                Pcoupltype               = Isotropic
>                tau_p                    = 1.0
>                compressibility          = 4.5e-5
>                ref_p                    = 1.0
> 
>                ; GENERATE VELOCITIES FOR STARTUP RUN
>                gen_vel                  = no    ; Assign velocities to
>                particles by taking them randomly from a Maxwell distribution
>                gen_temp                 = 300.0  ; Temperature to generate
>                corresponding Maxwell distribution
>                gen_seed                 = 9999   ; Seed for (semi) random
>                number generation.
> 
> 
>                ; OPTIONS constraints              = all-bonds
> 
>                Pooja
> 
> 
> 
> 
> 
> 
> 
>                On Fri, Jul 16, 2010 at 8:22 PM, Justin A. Lemkul
>                <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> wrote:
> 
> 
> 
>                   Sai Pooja wrote:
> 
>                       Hi,
> 
>                       I am getting these notes when I run grompp:
> 
>                       NOTE 3 [file Init/ffsb_init.top]:
>                        The largest charge group contains 12 atoms.
>                        Since atoms only see each other when the centers of
>                geometry of
>                       the charge
>                        groups they belong to are within the cut-off
>         distance, too
>                       large charge
>                        groups can lead to serious cut-off artifacts.
>                        For efficiency and accuracy, charge group should
>         consist
>                of a
>                       few atoms.
>                        For all-atom force fields use: CH3, CH2, CH, NH2, NH,
>                OH, CO2,
>                       CO, etc.
> 
>                       initialising group options...
>                       processing index file...
>                       Analysing residue names:
>                       There are:  3484      OTHER residues
>                       There are:    67    PROTEIN residues
>                       There are:     0        DNA residues
>                       There are:     0        RNA residues
>                       Analysing Protein...
>                       Analysing Other...
>                       Making dummy/rest group for Acceleration
>         containing 11343
>                elements
>                       Making dummy/rest group for Freeze containing
>         11343 elements
>                       Making dummy/rest group for VCM containing 11343
>         elements
>                       Number of degrees of freedom in T-Coupling group
>         Protein
>                is 1777.76
>                       Number of degrees of freedom in T-Coupling group
>                non-Protein is
>                       20898.23
>                       Making dummy/rest group for User1 containing 11343
>         elements
>                       Making dummy/rest group for User2 containing 11343
>         elements
>                       Making dummy/rest group for XTC containing 10450
>         elements
>                       Making dummy/rest group for Or. Res. Fit
>         containing 11343
>                elements
>                       Making dummy/rest group for QMMM containing 11343
>         elements
>                       T-Coupling       has 2 element(s): Protein non-Protein
>                       Energy Mon.      has 2 element(s): Protein non-Protein
>                       Acceleration     has 1 element(s): rest
>                       Freeze           has 1 element(s): rest
>                       User1            has 1 element(s): rest
>                       User2            has 1 element(s): rest
>                       VCM              has 1 element(s): rest
>                       XTC              has 2 element(s): Protein rest
>                       Or. Res. Fit     has 1 element(s): rest
>                       QMMM             has 1 element(s): rest
>                       Checking consistency between energy and charge
>         groups...
>                       Largest charge group radii for Van der Waals:
>         0.288, 0.263 nm
>                       Largest charge group radii for Coulomb:      
>         0.288, 0.263 nm
> 
>                       NOTE 4 [file nvtp.mdp]:
>                        The sum of the two largest charge group radii
>         (0.551009) is
>                       larger than
>                        rlist (2.000000) - rvdw (2.000000)
> 
>                       Can someone tell me how to correct these?
> 
> 
>                   Note 3 is explained in detail in the error message.
>          Beyond that,
>                   read about the group concept in the manual.
> 
>                   I've never seen Note 4 before, but a 2-nm cutoff is a
>         bit strange
>                   for a protein simulation.  Any reason you're using
>         such large
>                   cutoffs?  You may also want to provide your whole .mdp
>         file
>                to see
>                   if anyone can spot the underlying issue.
> 
>                   -Justin
> 
>                   --     ========================================
> 
>                   Justin A. Lemkul
>                   Ph.D. Candidate
>                   ICTAS Doctoral Scholar
>                   MILES-IGERT Trainee
>                   Department of Biochemistry
>                   Virginia Tech
>                   Blacksburg, VA
>                   jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
>         <http://vt.edu> | (540)
> 
>                231-9080
> 
>                   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
>                --         Quaerendo Invenietis-Seek and you shall discover.
> 
> 
>            --     ========================================
> 
>            Justin A. Lemkul
>            Ph.D. Candidate
>            ICTAS Doctoral Scholar
>            MILES-IGERT Trainee
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
>         -- 
>         Quaerendo Invenietis-Seek and you shall discover.
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

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

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