[gmx-users] CH3CN solvents breaking the periodic box

[Debashis Sahu]

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.*