[gmx-users] Charge grps and cut-off

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 17 13:25:23 CEST 2010



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>> 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>>> 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> | (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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> 
> 
> 
> -- 
> 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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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