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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
