Can you tell where I am going worng. Here I pasted my .itp file ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version
[ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_type mass charge ptype sigma epsilon opls_997 PA 0 100.0000 1.000 A 0.40000e-01 0.82890e-01 opls_998 NE 0 100.0000 -1.000 A 0.40000e-01 0.82890e-01 [ constraints ] ; i j func b0 kb 1 2 1 0.350000 Nilesh On Tue, July 27, 2010 12:38 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> still I am getting the same error. >> >> Now I added this two lines >> [ constraints ] >> 1 2 1 0.350000 >> >> > > Then you still have the directive in the wrong place. > > > -Justin > > >> On Tue, July 27, 2010 12:34 pm, Justin A. Lemkul wrote: >> >> >>> Nilesh Dhumal wrote: >>> >>> >>>> 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 >>>> >>>> >>> You don't define constraints with atom types, you use atom numbers. >>> See >>> the manual. >>> >>>> Fatal error: >>>> Syntax error - File solvent.itp, line 13 >>>> Last line read: >>>> ' [ constraints ]' >>>> Invalid order for directive constraints >>>> >>>> >>>> >>> Then you've put it in the wrong place. Like any other bonded term, >>> [constraints] belongs to the moleculetype to which the constraint is >>> to be applied. >>> >>> -Justin >>> >>> >>> >>>> 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 >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> -- >>> ======================================== >>> >>> >>> >>> 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 >>> >>> >>> >>> ======================================== >>> >>> >>> >>> >> >> >> > > -- > ======================================== > > > 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
