[gmx-users] CH3CN solvents breaking the periodic box

[Justin Lemkul]

On 5/25/15 2:07 PM, Debashis Sahu wrote:
> Dear Cara,
>                  Thank you for your answer. I have observed that when I have
> performed a NVT simulation for this mix solvent box (water 345 and
> acetonitrile 48), the solvent cavities are generated but in the NPT
> simulation interestingly there is no void cavity of solvent in solvent box.
> What is the reason behind it? If you have any idea about it please help
> me.........
>

Pressure closes the voids in NPT.  The NVT observations just indicate that the 
system is not equilibrated.

-Justin

> On Fri, May 15, 2015 at 12:31 PM, Cara Kreck <
> cara.kreck at student.curtin.edu.au> wrote:
>
>> 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
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>
>>>
>>>
>>> --
>>> *Debashis Sahu*
>>> *Central Salt and Marine Chemical Research Institute*
>>> *Bhavnagar, Gujarat*
>>> *India, 364002.*
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>

-- 
==================================================

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

==================================================