[gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory
Justin Lemkul
jalemkul at vt.edu
Wed Jan 30 14:36:11 CET 2013
On 1/30/13 6:01 AM, Shima Arasteh wrote:
> Dear users,
>
> I' d like to know if I need to check the npt.gro file time by time? I mean is it possible for npt.gro file to reach the equilibrated state and then again become unequilibrated?
>
Unlikely, unless there's something wrong with your run parameters or topology.
If you've done a sufficient job of equilibrating, nothing should go haywire
unless there's something more fundamentally wrong.
-Justin
>
> Thanks for your suggestions.
> Sincerely,
> Shima
>
>
> ________________________________
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Monday, January 28, 2013 2:32 PM
> Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up contains the
> ideas that will likely help you, e.g. smaller time step, more
> equilibration-friendly pressure coupling.
>
> Mark
>
> On Sun, Jan 27, 2013 at 1:59 PM, Shima Arasteh
> <shima_arasteh2001 at yahoo.com>wrote:
>
>>
>>
>> It is 15 ns of NPT equilibration and I have not got a proper npt output
>> yet to go to the MDrun. Because when I run the -mdrun command, I get fatal
>> error as water molecule can not be settled.
>>
>> I guess that the system might need more equilibration.
>>
>> These are the settings of my npt.mdp file. The force field which I use is
>> C36.
>>
>> integrator = md ; leap-frog integrator
>> nsteps =250000 ; 2 * 250000 = 500 ps
>> dt = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 1000 ; save coordinates every 0.2 ps
>> nstvout = 1000 ; save velocities every 0.2 ps
>> nstenergy = 1000 ; save energies every 0.2 ps
>> nstlog = 1000 ; update log file every 0.2 ps
>>
>> continuation = yes ; first dynamics run
>> constraint_algorithm = lincs ; holonomic constraints
>> constraints = h-bonds ; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>> ; Neighborsearching
>> ns_type = grid ; search neighboring grid cells
>> nstlist = 5 ; 10 fs
>> rlist = 1.2 ; short-range neighborlist cutoff (in nm)
>> rlistlong = 1.4
>> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
>> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
>> vdwtype = switch
>> rvdw_switch = 0.8
>> ; Electrostatics
>> coulombtype = PME ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order = 4 ; cubic interpolation
>> fourierspacing = 0.16 ; grid spacing for FFT
>> ; Temperature coupling is on
>> tcoupl = Nose-Hoover ; modified Berendsen thermostat
>> tc-grps = Protein POPC SOL_CL ; two coupling groups - more
>> accurate
>> tau_t = 0.5 0.5 0.5 ; time constant, in ps
>> ref_t = 310 310 310 ; reference temperature, one for each
>> group, in K
>> pcoupl = Parrinello-Rahman ; no pressure coupling in
>> NVT
>> pcoupltype = semiisotropic
>> tau_p = 4
>> ref_p = 1.01325 1.01325
>> compressibility = 4.5e-5 4.5e-5
>>
>> ; Periodic boundary conditions
>> pbc = xyz ; 3-D PBC
>> ; Dispersion correction
>> DispCorr = no ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = no ; assign velocities from Maxwell
>> distribution
>> ;gen_temp = 310 ; temperature for Maxwell distribution
>> ;gen_seed = -1 ; generate a random seed
>> nstcomm = 1
>> comm_mode = Linear
>> comm_grps = Protein_POPC SOL_CL
>>
>> Would you please give me any sugestions? What are the possible problems
>> might be considered?
>>
>>
>> Thanks for your suggestions.
>>
>> Sincerely,
>> Shima
>>
>>
>> ________________________________
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Sent: Sunday, January 6, 2013 9:15 AM
>> Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not
>> the same as in Trajectory
>>
>>
>>
>> On 1/6/13 12:33 AM, Shima Arasteh wrote:
>>> Do you mean that I re-run NPT step with the new index file and npt.gro
>> (which I got from the last NPT equilibration)? That's not clear to me yet.
>>>
>>
>> That's where I'd start. You may have to run the new configuration through
>> the entire equilibration protocol, though. Instability during MD often
>> indicates inadequate equilibration, so whatever your protocol is may not be
>> sufficient as is and may require greater time.
>>
>> -Justin
>>
>> -- ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> 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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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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