[gmx-users] CH3CN solvents breaking the periodic box
Cara Kreck
cara.kreck at student.curtin.edu.au
Fri May 15 09:01:34 CEST 2015
Hi Debashis,
I haven't looked at your trajectory but I suspect this will answer your question:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Cara
> Date: Fri, 15 May 2015 12:02:31 +0530
> From: debashis.sahu87 at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] CH3CN solvents breaking the periodic box
>
> Dear Justin,
> I have decreased the box size than previous box case. Now
> I have mentioned coupling between the system and the rest of mix solvent
> and ion. The trajectory of the MD is better than the earlier in this new
> box (water 345 and acetonitrile 48) cases. But there is a problem when I
> visualize the simulation in VMD, the system molecule fluctuate very
> suddenly from one direction to another and also tried to get out from the
> mix solvent box. I could not understand how to solve out the problem. If
> you have any idea about it please help me. I have attached the gro file and
> the corresponding xtc file.
> npt-1.xtc
> <https://docs.google.com/file/d/0Bz4vUvGCRemJRWR3SjMtNjFhRXc/edit?usp=drive_web>
>
> UN-F-3.gro
> <https://docs.google.com/file/d/0Bz4vUvGCRemJYzFqVnUwMlF3Qms/edit?usp=drive_web>
> with best regards,
> Debashis
>
> On Tue, Apr 21, 2015 at 2:35 AM, DEBASHIS SAHU <debashis.sahu87 at gmail.com>
> wrote:
>
> > Thanks Justin for your valuable answer..........
> > ------------------------------
> > From: Justin Lemkul <jalemkul at vt.edu>
> > Sent: 4/19/2015 8:48 PM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] CH3CN solvents breaking the periodic box
> >
> >
> >
> > On 4/18/15 2:33 AM, Debashis Sahu wrote:
> > > Dear Gromacs users,
> > > I have faced the simulation problem in
> > CH3CN
> > > solvent box. The box is broken in the NPT simulations and the solvent
> > > molecules also scatter. The trajectory and the pdb file is attached. I
> > can
> > > not understand why the simulation is not running well. If any one have an
> > > idea about this problem please help me.
> > >
> >
> > The box seems to be much too large for the number of molecules you have.
> > 128
> > solvent molecules will try to expand outward to fill the 5-nm cube you've
> > assigned.
> >
> > Don't couple everything separately.
> >
> > http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do
> >
> > -Justin
> >
> >
> > > npt.trr
> > > <
> > https://docs.google.com/file/d/0Bz4vUvGCRemJTWdmbnc1SGszX0E/edit?usp=drive_web
> > >
> > >
> > > UN-F-2.pdb
> > > <
> > https://docs.google.com/file/d/0Bz4vUvGCRemJZ3NhSG1iNkFxQkE/edit?usp=drive_web
> > >
> > >
> > >
> > > I have .mdp file of the energy minimization is as follow:
> > >
> > > integrator = steep ; Algorithm (steep = steepest descent minimization)
> > > emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0
> > > kJ/mol/nm
> > > emstep = 0.01 ; Energy step size
> > > nsteps = 50000 ; Maximum number of (minimization) steps to perform
> > >
> > > ; Parameters describing how to find the neighbors of each atom and how to
> > > calculate the interactions
> > > nstlist = 1 ; Frequency to update the neighbor list and long range forces
> > > ns_type = grid ; Method to determine neighbor list (simple, grid)
> > > rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
> > > coulombtype = PME ; Treatment of long range electrostatic interactions
> > > rcoulomb = 1.0 ; Short-range electrostatic cut-off
> > > rvdw = 1.0 ; Short-range Van der Waals cut-off
> > > pbc = xyz ; Periodic Boundary Conditions (yes/no)
> > >
> > >
> > > The .mdp file of NPT is as below:
> > >
> > > title = NPT Equilibration
> > > define = -DPOSRES ; position restrain
> > > ; Run parameters
> > > integrator = md ; leap-frog integrator
> > > nsteps = 200000 ; 2 * 50000 = 100 ps
> > > dt = 0.002 ; 2 fs
> > > ; Output control
> > > nstxout = 100 ; save coordinates every 2 ps
> > > nstvout = 100 ; save velocities every 2 ps
> > > nstenergy = 100 ; save energies every 2 ps
> > > nstlog = 100 ; update log file every 2 ps
> > > nstcalcenergy = 1
> > > ; Bond parameters
> > > continuation = no ; Initial simulation
> > > constraint_algorithm = lincs ; holonomic constraints
> > > constraints = all-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 cels
> > > nstlist = 5 ; 10 fs
> > > rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> > > rcoulomb = 1.0 ; short-range electrostatic cutoff (in
> > nm)
> > > rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> > > ; 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 = V-rescale ; Weak coupling for initial
> > > equilibration
> > > tc-grps = UNK F SOL ; two coupling groups - more accurate
> > > tau_t = 0.1 0.1 0.1 ; time constant, in ps
> > > ref_t = 300 300 300 ; reference temperature, one for each
> > > group, in K
> > > ; Pressure coupling is on
> > > pcoupl = Parrinello-Rahman ; Pressure coupling on in
> > NPT,
> > > also weak coupling
> > > pcoupltype = isotropic ; uniform scaling of x-y-z box
> > vectors
> > > tau_p = 2.0 ; time constant, in ps
> > > ref_p = 1.0 ; reference pressure (in bar)
> > > compressibility = 4.5e-5 ; isothermal compressibility, bar^-1
> > > refcoord_scaling = com
> > > ; Periodic boundary conditions
> > > pbc = xyz ; 3-D PBC
> > > ; Dispersion correction
> > > DispCorr = EnerPres ; account for cut-off vdW scheme
> > > ; Velocity generation
> > > gen_vel = no ; Velocity generation is off
> > > gen_temp = 300 ; temperature for velocity generation
> > > gen_seed = -1 ; random seed
> > > ; COM motion removal
> > > ; These options remove COM motion of the system
> > > nstcomm = 10
> > > comm-mode = Linear
> > > comm-grps = System
> > >
> > > with warm regards,
> > > *Debashis Sahu*
> > > *Central Salt and Marine Chemical Research Institute*
> > > *Bhavnagar, Gujarat*
> > > *India, 364002.*
> > >
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
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>
>
> --
> *Debashis Sahu*
> *Central Salt and Marine Chemical Research Institute*
> *Bhavnagar, Gujarat*
> *India, 364002.*
> --
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