There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt find them
2013/4/11 Justin Lemkul <[email protected]> > On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım <[email protected]> > 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 <[email protected]> > > > > > On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım <[email protected]> > > > 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 <[email protected]> > > > > > > > > > On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım < > [email protected] > > > > > > > > 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 [email protected] > > > > > 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 [email protected]. > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > > > > > > -- > > > > Ahmet Yıldırım > > > > -- > > > > gmx-users mailing list [email protected] > > > > 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 [email protected]. > > > > * 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 [email protected] > > > 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 [email protected]. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > -- > > Ahmet Yıldırım > > -- > > gmx-users mailing list [email protected] > > 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 [email protected]. > > * 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet Yıldırım -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? 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