[gmx-users] Slab shifts out of the simulation box

[Justin Lemkul]

On 9/17/19 11:17 AM, Mohammed Hamza wrote:
> Dear Sohaib
>
> I did use all-bonds and was the same. I wonder why the slab shifts

You have an "infinite" molecule that you're trying to wrap into a finite 
volume. There is no single, unambiguous way to do that. Note that there 
is no such thing as "outside" in a periodic system, so there is no 
problem aside from visualization. You can recenter with trjconv, though 
you will get the same kind of "inconsistent shift" warnings, which 
really should be disabled in the code in the case of periodic molecules.

-Justin

> Best Regards,
> Mohammed
>
> On Tue, Sep 17, 2019 at 10:08 AM Sohaib. Mohammed <
> sohaibmohammed10 at gmail.com> wrote:
>
>> It is better to use CLAYff forcefield for your mineral surface and generate
>> the non-bonded parameters for solid-hydrocarbons interactions. You can use
>> CHARMM27 to generate the topology for your hydrocarbons.
>> Why did you use constraints only for h-bonds, how about all bonds.
>>
>> Best,
>> Sohaib
>>
>> On Tue, Sep 17, 2019 at 9:46 AM Mohammed Hamza <
>> mohammedhamzakhalaf at gmail.com> wrote:
>>
>>> Dear GMX users
>>>
>>> I'm simulating a mixture of hydrocarbons on a slab of mineral using
>>> CHARMM27 ff. The topology of the slab was generated using the interface
>>> forcefield script.
>>> I see the slab shifts out of the simulation box (shown in the links
>> below)
>>> and get "There were 724 inconsistent shifts. Check your topology".
>>> I check the topology and I don't see anything unusual.
>>> Any ideas what is going on?
>>>
>>> Thanks in advance
>>>
>>>
>>> https://www.dropbox.com/s/hppbfa7pse6htem/final%20slab.png?dl=0
>>> https://www.dropbox.com/s/hk3d0mrkew7c55s/initial%20box.png?dl=0
>>>
>>> Here is the mdp that I used
>>>
>>> ; Run parameters
>>> integrator     = md ; leap-frog integrator
>>> nsteps     = 50000        ; 2 * 25000000 = 50000 ps
>>> dt     = 0.001 ; 2 fs
>>> ; Output control
>>> nstxout = 500 ; save coordinates every 1.0 ps
>>> nstvout = 500 ; save velocities every 1.0 ps
>>> nstenergy = 500 ; save energies every 1.0 ps
>>> nstlog = 500 ; update log file every 1.0 ps
>>> nstxout-compressed = 500
>>> ; Bond parameters
>>> constraint_algorithm        = lincs    ; holonomic constraints
>>> constraints             = h-bonds
>>> lincs_iter            = 1    ; accuracy of LINCS
>>> lincs_order            = 4    ; also related to accuracy
>>> ; Neighborsearching
>>> cutoff-scheme       = Verlet
>>> ns_type    = grid ; search neighboring grid cells
>>> nstlist    = 10        ; 20 fs, largely irrelevant with Verlet scheme
>>> rcoulomb    = 1.2 ; short-range electrostatic cutoff (in nm)
>>> rvdw    = 1.2 ; 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        ; modified Berendsen thermostat
>>> tc-grps = System        ; two coupling groups - more accurate
>>> tau_t = 0.1                ; time constant, in ps
>>> ref_t = 350                ; reference temperature, one for each group,
>> in
>>> K
>>>
>>> ; Periodic boundary conditions
>>> pbc     = xyz ; 3-D PBC
>>> periodic-molecules   = yes
>>> ; Dispersion correction
>>> DispCorr     = no
>>> ; Velocity generation
>>> gen_vel      = no ; Velocity generation is off
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Justin A. Lemkul, Ph.D.
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