On Thu, Apr 11, 2013 at 7:28 AM, Ahmet yıldırım <ahmedo...@gmail.com> wrote:
> There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt > find them > > They're there. The tip5p.gro file is in $GMXLIB and tip5p.itp is in several force field subdirectories. $ ls -l *.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber03.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber94.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber96.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber99.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber99sb.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber99sb-ildn.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amberGS.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 charmm27.ff/tip5p.itp -rw-r--r-- 1 jalemkul jalemkul 1434 Nov 27 20:24 oplsaa.ff/tip5p.itp -Justin > > 2013/4/11 Justin Lemkul <jalem...@vt.edu> > > > On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım <ahmedo...@gmail.com> > > wrote: > > > > > I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from > > > gromacs 4.0.7. are they wrong? > > > > > > > > Well, they trigger a fatal error... > > > > Yes, they are wrong and newer versions of Gromacs are correct. > > > > -Justin > > > > > > > > > > 2013/4/11 Justin Lemkul <jalem...@vt.edu> > > > > > > > On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım <ahmedo...@gmail.com > > > > > > wrote: > > > > > > > > > Dear Justin, > > > > > > > > > > I copied to gmx.ff it. You know the tip5p shows the general shape > of > > > the > > > > > 5-site water models but the spc shows the general shape of the > 3-site > > > > water > > > > > models. Therefore I need tip5p.itp. > > > > > > > > > > > > > Is there going to be a protein in the system, as well? If so, gmx.ff > > is a > > > > poor choice and I would still maintain that despite any possible > > > > improvement in water model (and none of them are perfect), it's not a > > > > proper combination. If you're simulating pure water, the choice of > > parent > > > > force field is largely irrelevant. > > > > > > > > > > > > > How can you get it? > > > > > > > > > > > > > > I have no idea why your tip5p.itp is wrong. The atom type should be > MW > > > for > > > > both LP1 and LP2, as I said before. Fix the atom types and the > problem > > > > should go away. > > > > > > > > -Justin > > > > > > > > > > > > > > > > > > 2013/4/11 Justin Lemkul <jalem...@vt.edu> > > > > > > > > > > > On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım < > > ahmedo...@gmail.com > > > > > > > > > > wrote: > > > > > > > > > > > > > Dear users, > > > > > > > > > > > > > > I am trying MD simulation of tip5p water model. I am getting > > Fatal > > > > > > > Error:Atomtype LP1 not found. > > > > > > > There isnt LP in atomtypes.atp file. Which one corresponds to > LP1 > > > and > > > > > LP2 > > > > > > > atoms in atomtypes.atp file? > > > > > > > (I am using Gromacs 4.5.5) > > > > > > > > > > > > > > > > > > > > > usr/share/gromacs/top/gmx.ff/tip5p.itp > > > > > > > ... > > > > > > > [ atoms ] > > > > > > > ; id at type res nr residu name at name cg nr > > > > charge > > > > > > > 1 OW 1 SOL OW 1 > > > > 0 > > > > > > > 2 HW1 1 SOL HW1 > > 1 > > > > > > > 0.241 > > > > > > > 3 HW2 1 SOL HW2 1 > > > > > > 0.241 > > > > > > > 4 LP1 1 SOL LP1 1 > > > > > > -0.241 > > > > > > > 5 LP2 1 SOL LP2 1 > > > > > > -0.241 > > > > > > > .... > > > > > > > > > > > > > > > > > > > > It looks like someone has erroneously modified your files. The > > TIP5P > > > > > model > > > > > > should not be included in gmx.ff (Gromos force fields should be > > used > > > > with > > > > > > SPC), and the atom type for both LP1 and LP2 should be MW. > > > > > > > > > > > > -Justin > > > > > > > > > > > > -- > > > > > > > > > > > > ======================================== > > > > > > > > > > > > Justin A. Lemkul, Ph.D. > > > > > > Research Scientist > > > > > > Department of Biochemistry > > > > > > Virginia Tech > > > > > > Blacksburg, VA > > > > > > jalemkul[at]vt.edu | (540) > > > > > > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > > > > > > > ======================================== > > > > > > -- > > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > > * 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 gmx-users-requ...@gromacs.org. > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Ahmet Yıldırım > > > > > -- > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > * 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 gmx-users-requ...@gromacs.org. > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > ======================================== > > > > > > > > Justin A. Lemkul, Ph.D. > > > > Research Scientist > > > > Department of Biochemistry > > > > Virginia Tech > > > > Blacksburg, VA > > > > jalemkul[at]vt.edu | (540) > > > > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > > > ======================================== > > > > -- > > > > gmx-users mailing list gmx-users@gromacs.org > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > * 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 gmx-users-requ...@gromacs.org. > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > -- > > > Ahmet Yıldırım > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * 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 gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > -- > > > > ======================================== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) > > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * 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 gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Ahmet Yıldırım > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists