I put the constraints on PA-NE to keep the bond length 3.5 A. After calculating the g_dist I noted that the bond length is atound 5.5 A. Can you tell why its taking 5.5 A. If I difine contraints=all-bonds in mdp file then it shows 3.5 A proper bond length. Can u tell where is the problem. Here I pasted the .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 [ bondtypes ] ; i j func b0 kb PA NE 1 0.350000 000000 [ moleculetype ] ; name nrexcl ABC 2 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 opls_997 1 ABC PA 1 1.0000 100.0000 2 opls_998 1 ABC NE 1 -1.0000 100.000 [ constraints ] ; i j func b0 kb 1 2 1 0.350000 On Tue, July 27, 2010 7:07 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> 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 >> >> >> > > As I said before (and is explained in the manual), [constraints], like > any other bonded parameter, must belong to a [moleculetype], which you > have not defined here. You've got atom types and force field information, > but no molecule to which the constraints are applied. > > -Justin > > >> 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 >>> >>> >>> >>> >> >> >> > > -- > ======================================== > > > 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
