I am using opls force field. I have solvent.itp file. I added follwing line in my solvent.itp file. [ constraints ] opls_997 opls_998 1 0.350000 I am getting the following error
Fatal error: Syntax error - File solvent.itp, line 13 Last line read: ' [ constraints ]' Invalid order for directive constraints Nilesh On Tue, July 27, 2010 11:29 am, Justin A. Lemkul wrote: > > Yes, if you define it in a [ constraints ] directive, and use > "constraints = > none" in your .mdp file, so that other bonds will not be converted to > constraints, but the one you explicitly set in the topology will be used. > > > -Justin > > > Nilesh Dhumal wrote: > >> Can I put constraint on selected bond? >> Nilesh >> >> >> On Sun, July 25, 2010 11:33 pm, Vitaly Chaban wrote: >> >>> 1. Using freezegrps is not generally a good idea to fix a bond >>> length. Look at the constraints mechenism better. Or just try a bigger >>> force constant in topology. >>> >>> 2. NPT and freezegrps do not interact correctly, since freezegrps >>> just freezes any changes of atom positions, so they are not rescaled >>> even if the box size is changed in NPT. >>> >>> 3. Anyway, I think you have defined incorrect groups if your atoms of >>> interest are still movable. Check a diffusion constant of your >>> bonded atoms, it should be zero in the case of freezegrps. >>> >>> Dr. Vitaly Chaban >>> >>> >>> >>> >>> >>> >>>> I am trying to freeze a bond (3.5 A) in my system. I used the >>>> index file to define group and I added this two lines in my .mdp >>>> file. >>>> >>>> freezegrps = PA NE freezedim = Y Y Y Y Y Y >>>> >>>> I used g_dist to verify the distance between the freezing atoms. >>>> During >>>> the NVT simulation the distace is around 3.449 A and its constant >>>> though out the simulation. For NPT simulation the distance varies >>>> from 3.449 to >>>> 3.1. >>>> Can you tell why distance changes in NPT not in NVT. >>>> How can I freeze a bond om NPT simulation? >>>> >>>> >>>> >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>> >>> >>> >>> >> >> > > -- > ======================================== > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://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/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/mailing_lists/users.php > > > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
