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

[Justin Lemkul]

On 1/3/13 2:01 PM, James Starlight wrote:
> 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 ?
>

Not from the .rtp file, but the .top is overriding the contents of ffnonbonded.itp.

-Justin

-- 
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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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