[gmx-users] A charge group moved too far between two
Justin A. Lemkul
jalemkul at vt.edu
Fri Aug 21 16:50:00 CEST 2009
Chih-Ying Lin wrote:
> Hi
> I was currently updatiing the 3.3.3 version to 4.0.5 version.
> My system is "one protein + TIP3P water".
> The protein structure is from 6LYZ.pdb
>
>
>
> The ,gro file and .top file are created from pdb2gmx.
> Then, I do the following steps,
> Energy minimization of the structure (vacuum)
> Periodic boundary conditions
> Solvent addition
> Addition of ions: counter charge
> Energy minimization of the solvated system
> Relaxation of solvent and hydrogen atom positions: Position restrained MD
>
>
>
> This "one protein + TIP3P water" system is running no problems with 3.3.3.
> But, the Fetal Error "A charge group moved too far between two" comes
> from 4.0.5.
>
>
> All the commands are from the tutorials =>
> http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
>
>
> Although my system is blowing, which is suggested by
> oldwiki.gromacs.org, i think the protein structure is OK, I have no
> ideas about which steps I was doing wrong.
>
> Any ideas about this?
>
Watch the trajectory. See where your structure is getting distorted or where
bad contacts might be occurring.
-Justin
>
> Thank you
> Lin
>
>
>
>
>
>
>
> Chih-Ying Lin wrote:
>> Hi
>> In the system, one lysozyme + TIP3P water.
>>
>> After the two commands,
>> grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr
>> mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR
>>
>>
>>
>>
>> pr.mdp, minim.mdp and the error information is as follows.
>> nsteps = 5000 ; Maximum number of (minimization) steps
>> How to solve the problem?
>>
>> Thank you
>> Lin
>>
>>
>>
>> -------------------------------------------------------
>> Program mdrun_mpi, VERSION 4.0.5
>> Source code file: domdec.c, line: 3651
>>
>> Fatal error:
>> A charge group moved too far between two domain decomposition steps
>> This usually means that your system is not well equilibrated
>> -------------------------------------------------------
>>
>>
>
> Well, you're being given a pretty explicit hint. This is a very useful error
> message. You're system is blowing up. I'd point to the relevant wiki site, but
> it appears that oldwiki.gromacs.org is not operating...
>
> In any case, better minimization and/or equilibration is necessary, as mdrun has
> told you.
>
> -Justin
>
>>
>>
>> ; VARIOUS PREPROCESSING OPTIONS
>> title =
>> cpp = /lib/cpp
>> include =
>> define = -DPOSRES
>>
>> ; RUN CONTROL PARAMETERS
>> integrator = md
>> tinit = 0
>> dt = 0.001
>> nsteps = 5000
>> nstcomm = 0
>>
>> ; OUTPUT CONTROL OPTIONS
>> nstxout = 0
>> nstvout = 0
>> nstfout = 0
>> nstlog = 10
>> nstenergy = 1
>> nstxtcout = 0
>> xtc_precision = 1000
>> xtc-grps = System
>> energygrps = Protein Non-Protein
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> nstlist = 5
>> ns-type = Grid
>> pbc = xyz
>> rlist = 0.9
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> coulombtype = Reaction-Field
>> rcoulomb = 1.4
>> epsilon_rf = 78
>> epsilon_r = 1
>> vdw-type = Cut-off
>> rvdw = 1.4
>>
>> ; Temperature coupling
>> Tcoupl = Berendsen
>> tc-grps = Protein Non-Protein
>> tau_t = 0.1 0.1
>> ref_t = 200 200
>>
>> ; Pressure coupling
>> Pcoupl = No
>>
>> ; GENERATE VELOCITIES FOR STARTUP RUN
>> gen_vel = yes
>> gen_temp = 200.0
>> gen_seed = 1735
>>
>> ; OPTIONS FOR BONDS
>> constraints = all-bonds
>> constraint-algorithm = Lincs
>> unconstrained-start = no
>> lincs-order = 4
>> lincs-iter = 1
>> lincs-warnangle = 30
>>
>>
>>
>>
>>
>>
>> ; LINES STARTING WITH ';' ARE COMMENTS
>> title = Minimization of Lysozyme (1LW9.pdb) ; Title of run
>>
>> ; The following lines tell the program the standard locations where to
>> find cert
>> ain files
>> cpp = /lib/cpp ; Preprocessor
>>
>> ; Definea can be used to control processes
>> define = -DFLEXIBLE
>>
>> ; Parameters describing what to do, when to stop and what to save
>> integrator = steep ; Algorithm (steep = steepest descent
>> minimizati
>> on)
>> emtol = 1.0 ; Stop minimization when the maximum
>> force < 1.0
>> kJ/mol
>> nsteps = 5000 ; Maximum number of (minimization) steps
>> to perf
>> orm
>> nstenergy = 1 ; Write energies to disk every nstenergy
>> steps
>> energygrps = System ; Which energy group(s) to write to disk
>>
>> ; Parameters describing how to find the neighbors of each atom and how
>> to calcul
>> ate the
>> interactions
>> nstlist = 5 ; Frequency to update the neighbor list
>> and long
>> range forces
>> ns_type = simple ; Method to determine neighbor list
>> (simple, gri
>> d)
>> rlist = 1.0 ; Cut-off for making neighbor list
>> (short range
>> forces)
>> coulombtype = cut-off ; Treatment of long range electrostatic
>> interact
>> ions
>> rcoulomb = 1.0 ; long range electrostatic cut-off
>> rvdw = 1.0 ; long range Van der Waals cut-off
>> constraints = none ; Bond types to replace by constraints
>> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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