[gmx-users] Re: Simulation of 2D lattice model
jmsstarlight at gmail.com
Thu Jan 3 20:01:25 CET 2013
thanks again for explanation. By the way if I define in topology top
LJ params like
; Include forcefield parameters
[ atomtypes ]
;name at.num mass charge ptype c6 c12
CH2 6 0.000 0.000 A 0.0074684164 3.3965584e-05
CH3 6 0.000 0.000 A 0.0096138025 2.6646244e-05
[ nonbond_params ]
; i j func c6 c12
CH3 CH2 1 0.008473481 3.0084136e-05
[ moleculetype ]
; Name nrexcl
i've obtain warns
WARNING 1 [file lattice.top, line 23]:
Overriding atomtype CH2
WARNING 2 [file lattice.top, line 24]:
Overriding atomtype CH3
does it mean that the params from topology.top will be used instead of
RTP file ?
2013/1/3, Justin Lemkul <jalemkul at vt.edu>:
> On 1/3/13 11:49 AM, James Starlight wrote:
>> I've made new lattice model in GROMOS united atoms. I've used 2 nodes
>> - CH2 (ca) for atom with 3 bonds as well as CH1 (CB) for boundary
>> atoms with 2 bonds to adjacent nodes.
> I'm assuming you've simply switched the atom types here. A CH2 should not
> 3 other bonds.
>> That system is considerably rigid in comparison to the lattice which
>> I've simulated in OPLS all atom ff.
>> Does it possible to change VDW(LJ) parameters for both nodes in the
>> top file or should I modify existing atom types in ffnonbonded ?
> You can do anything you like, but you'd better have good justification for
> Making ad hoc changes to force fields that were not necessarily designed to
> what you think it should is generally very unwise. Whatever you do, make
> changes in a local copy of the force field so you don't screw up other
> simulations later on, or even better, make a special [atomtypes] directive
> your .top file.
>> How I could prevent rotation of the lattice as the whole object ? (
>> simulation in vacuum in NVT) without any posres ?
> I can't think of a way to do this, nor would it have any real functional
> purpose. You can remove rotation and translation afterwards with trjconv.
>> Its not possible to use very small box dimensions due to the rvdv= 1.4
>> in gromos ff
>> (if I define box vectors compatible with the size of the lattice I've
>> obtain error in grompp)
> If you're running in vacuo, you should turn off PBC and use infinite
> otherwise you likely will have periodicity artifacts and you are not truly
> simulating in vacuo.
>> Also in connection to the above question with the box size I also
>> wounder like to know how I could use ; periodic_molecules options
>> with such lattice which asymmetric on left and right boundaries (
>> picture http://imageshack.us/photo/my-images/543/lattice.png/ ) ?
> Some boxes have hexagonal cross-sections (see the manual) that might be
> In a basic sense, all you need to have is atoms that should be bonded to
> another through a periodic boundary should be separated by one bond length
> half a bond length on either side of the box) and make sure these bonds are
> added to the topology (probably by hand). Then the periodic_molecules
> works its magic and you have an infinite lattice.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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