[gmx-users] sovation with tip3p
Peter C. Lai
pcl at uab.edu
Wed Jul 11 18:27:37 CEST 2012
This is not really true. It is perfectly appropriate to use spc216.gro with
the tip3p water model since any spacing differences will settle out during
npt equilibration anyway.
On 2012-07-11 02:28:52PM +0430, amir abbasi wrote:
> Hi,
> I had this problem too.
> unfortunately gmx not included tip3p model of water anymore.
> You have two ways.
> 1.using spc216 that gmx offers or
> 2.Buil your system in Ambertools (leap) and convert your .prmtop and
> .inpcrd files to .top and .gro
> if you persist on using tip3p water model i suggest you to pick second way.
> Regards,
> Amir
>
>
> Subject: [gmx-users] sovation with tip3p
>
> Hi all,
>
> I'm going to do the step 3 in Justin's tutorial (Lysozyme in water) .
> In this step, the solvation is accomplished through this command:
> genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
>
> in which that spc216.gro is used. In first step I had used the TIP3P
> water model, here I'd rather to call TIP3P too. But there is not
> tip3p.gro in share/top .
>
> I would appreciate you if you give me any suggestion.
> Thanks in advance.
>
>
>
>
> Sincerely,
> Shima
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--
==================================================================
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
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