I am going to put solvent arond this solute. I want to freeze the distance only for solute not for solvent. Nilesl
On Fri, July 30, 2010 10:45 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> 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. > > From your original post some time ago, it was not clear that you only had > one bond to deal with. If this is the case, then your approach sounds > fine, just use a normal [ bonds ] directive and set "constraints = > all-bonds." As you say, that works, so I don't see what the problem is. > Are you going to be developing > a more complex system for which you don't want other bonds constrained, > just the one defined below? Another approach would be a distance > restraint, but I don't believe that will absolutely fix the distance, > unless your tolerance is set very strictly. > > -Justin > > >> 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 >>> >>> >>> >>> >> >> >> >> > > -- > ======================================== > > > 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
