[gmx-users] Charge grps and cut-off
Sai Pooja
saipooja at gmail.com
Sat Jul 17 13:52:19 CEST 2010
If gromacs assumes the aminoacid residues as charge groups by default then I
have many residues which have 12 atoms since I am using an all-atom force
field-charmm27(counting H).
Is there a way to define charge groups?
On Sat, Jul 17, 2010 at 7:41 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org
>> >>
>> <mailto:gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>>>
>>
>>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list.
>> Use the www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>
>> <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>>
>> <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>
>> <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>>>.
>>
>> Can't post? Read
>> http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> -- 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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/searchbefore
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>
>> <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>>.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> -- 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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Quaerendo Invenietis-Seek and you shall discover.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100717/8145c90a/attachment.html>
More information about the gromacs.org_gmx-users
mailing list