[gmx-users] Re: Simulation of 2D lattice model

[James Starlight]

Justin,

thanks again for explanation. By the way if I define in topology top
LJ params like

; Include forcefield parameters
#include "gromos53a5.ff/forcefield.itp"

[ 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
ICE                 3

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 ?

James

2013/1/3, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 1/3/13 11:49 AM, James Starlight wrote:
>> Justin,
>>
>>
>> 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
> have
> 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
> it.
> Making ad hoc changes to force fields that were not necessarily designed to
> do
> 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
> in
> 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
> cutoffs,
> 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
> useful.
>   In a basic sense, all you need to have is atoms that should be bonded to
> one
> another through a periodic boundary should be separated by one bond length
> (i.e.
> 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
> option
> works its magic and you have an infinite lattice.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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