[gmx-users] water model

 Dear gmx friends, Is there the best water model for each force fields? Which options are supposed to be noticed in applying the best water model. I need to tell you that I apply C36 in my simulations. Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] water model

For CHARMM the typical water model is TIP3P, although I tend to use TIPS3P since it's been reported on the mailing list to give better interactions with bilayers. (Also easier to pass by picky reviewers at the expense of ns/day, obviously). The following thread may be helpful too:

[gmx-users] water model purpose?

Hi, pdb2gmx -f 1LYD.pdb -water tip3p Why is -water tip3p command ( tip3p water model) used? What the purpose? Afterwards, genbox command is already added to solvent water as the following: genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro Thanks -- Ahmet YILDIRIM --

Re: [gmx-users] water model purpose?

On 23/11/2010 8:35 PM, ahmet yıldırım wrote: Hi, pdb2gmx -f 1LYD.pdb -water tip3p Why is -water tip3p command ( tip3p water model) used? What the purpose? This chooses the water model embedded in the system topology written by pdb2gmx. Afterwards, genbox command is already added to

Re: [gmx-users] water model and force field

varsha gautham wrote: Dear gmx-users, Am doing a simulation of DPPC bilayer with a polymer. I read from various papers that SPC is the best water model for lipids and GROMOS 87 is the best force field adapted for the lipids. So i made use of SPC and gromos 87 in my simulation .But am not

[gmx-users] water model and force field

Dear gmx-users, Am doing a simulation of DPPC bilayer with a polymer. I read from various papers that SPC is the best water model for lipids and GROMOS 87 is the best force field adapted for the lipids. So i made use of SPC and gromos 87 in my simulation .But am not clear with GROMOS 87 file

[gmx-users] Water model = amber port to gromacs ? = OR

HI The thing is the definition of atom type, OW and H in gromos 96 are different from tip3p.itp, OWT3, HW. same thing as other tip*p.itp. How to fix this? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Water model = amber port to gromacs ? = OR Only SPC ?

Hi Can the TIP3P water model used under gromos 96 force field? Although the Amber_TIP3P.top can port to gromacs, it based on the amber99 force field. I read about the imcompatibility of any two force field parameters from different sources, such as amber99 and gromos96. Is Gromacs only limited

Re: [gmx-users] Water model = amber port to gromacs ? = OR Only SPC ?

Chih-Ying Lin wrote: Hi Can the TIP3P water model used under gromos 96 force field? Although the Amber_TIP3P.top can port to gromacs, it based on the amber99 force field. I read about the imcompatibility of any two force field parameters from different sources, such as amber99 and gromos96.

Re: [gmx-users] Water model = amber port to gromacs

Chih-Ying Lin wrote: Hi Water model = amber port to gromacs The two steps are shown on the archive. 1. #include ffamber_tip*pin the .top file 2. include an #ifdef_FF_AMBER statement in tip*p.itp If you want others' opinions for free, please provide links - and test them first to see that

[gmx-users] Water model = amber port to gromacs

HI Here are the links. Water model = amber port to gromacs http://www.gromacs.org/pipermail/gmx-users/2007-June/027817.html http://www.gromacs.org/pipermail/gmx-users/2007-June/027823.html http://www.gromacs.org/pipermail/gmx-users/2007-June/027840.html The two steps are shown on the above

Re: [gmx-users] Water model = amber port to gromacs

Chih-Ying Lin wrote: HI Here are the links. Water model = amber port to gromacs http://www.gromacs.org/pipermail/gmx-users/2007-June/027817.html http://www.gromacs.org/pipermail/gmx-users/2007-June/027823.html http://www.gromacs.org/pipermail/gmx-users/2007-June/027840.html The two

[gmx-users] Water model = amber port to gromacs

Hi Water model = amber port to gromacs The two steps are shown on the archive. 1. #include ffamber_tip*pin the .top file 2. include an #ifdef_FF_AMBER statement in tip*p.itp Should I also #include ffamber99.tip in the .top file? Thank you Lin