> > > On 7/26/12 7:06 AM, [email protected] wrote: >>> >>> >>> On 7/26/12 6:07 AM, [email protected] wrote: >>>>> On 26/07/2012 6:47 PM, [email protected] >>>>> wrote: >>>>>> Ho, >>>>>> first I minimize my structure. This is the corresponding mdp file: >>>>>> >>>>>> define = -DPOSRES >>>>>> integrator = steep >>>>>> emtol = 10 >>>>>> nsteps = 1500 >>>>>> nstenergy = 1 >>>>>> energygrps = System >>>>>> coulombtype = PME >>>>>> rcoulomb = 0.9 >>>>>> rvdw = 0.9 >>>>>> rlist = 0.9 >>>>>> fourierspacing = 0.12 >>>>>> pme_order = 4 >>>>>> ewald_rtol = 1e-5 >>>>>> pbc = xyz >>>>>> >>>>>> >>>>>> and then I run a md run. This is the corresponding mdp file: >>>>>> >>>>>> define = -DPOSRES >>>>>> integrator = md >>>>>> dt = 0.001 >>>>>> nsteps = 5000 >>>>>> nstxout = 100 >>>>>> nstvout = 0 >>>>>> nstfout = 0 >>>>>> nstlog = 1000 >>>>>> nstxtcout = 500 >>>>>> nstenergy = 5 >>>>>> energygrps = Protein Non-Protein >>>>>> nstcalcenergy = 5 >>>>>> nstlist = 10 >>>>>> ns-type = Grid >>>>>> pbc = xyz >>>>>> rlist = 0.9 >>>>>> coulombtype = PME >>>>>> rcoulomb = 0.9 >>>>>> rvdw = 0.9 >>>>>> fourierspacing = 0.12 >>>>>> pme_order = 4 >>>>>> ewald_rtol = 1e-5 >>>>>> gen_vel = yes >>>>>> gen_temp = 200.0 >>>>>> gen_seed = 9999 >>>>>> constraints = all-bonds >>>>>> tcoupl = V-rescale >>>>>> tc-grps = Protein Non-Protein >>>>>> tau_t = 0.1 0.1 >>>>>> ref_t = 298 298 >>>>>> pcoupl = no >>>>>> >>>>>> >>>>>> >>>>>> In my topology file I include the restraint files like this: >>>>>> >>>>>> ; Include Position restraint file >>>>>> #ifdef POSRES >>>>>> #include "posre.itp" >>>>>> #endif >>>>>> >>>>>> #ifdef POSRES >>>>>> #include "posre_memb.itp" >>>>>> #endif >>>>> >>>>> This won't work for multiple [moleculetype] entries. See >>>>> http://www.gromacs.org/Documentation/How-tos/Position_Restraints >>>>> >>>>>> >>>>>> >>>>>> I just recognize that there is a "DPOSRES" in the mdp files and a >>>>>> "POSRES" >>>>>> in my topology file. Is this the problem. Do I have to write it the >>>>>> same >>>>>> way in the several files? >>>>> >>>>> http://www.gromacs.org/Documentation/Include_File_Mechanism >>>>> >>>>> Mark >>>> >>>> >>>> I just see that the [ position_restraints ] part is included under the >>>> [dihedral] and not between the [moleculetype] and the [atom] part. And >>>> according to the site you wrote me this is a problem, right? But this >>>> was >>>> done by gromacs itself. Shell I write it to the [moleculetype] part? >>>> >>> >>> A [position_restraints] directive belongs to the [moleculetype] in >>> which >>> it is >>> declared. The original location of the #include statement produced by >>> Gromacs >>> is correct; it follows sequentially within the protein [moleculetype]. >>> Your >>> inclusion of the membrane restraint file within the protein >>> [moleculetype] >>> is, >>> however, incorrect. >>> >>>> But I can not see why it can not work that I have 2 restriction files? >>>> Can >>>> you please explain it to me? >>>> >>> >>> You can have two restraint files for different [moleculetypes] but they >>> must be >>> organized as such. >> >> okey. So the whole thing with [atoms], [bonds], [dihedral] all contains >> to >> the entry in [moleculetype] , right? >> > > Any directive belongs to the [moleculetype] that immediately precedes it. > Once > a new [moleculetype] is declared (either directly or indirectly via > #include > mechanism), you're working with a different molecule. > >> But directly before I include the membrane restriction file I include >> the >> membrane definition: >> >> #include "amber03.ff/dum.itp" >> #ifdef POSRES >> #include "posre_memb.itp" >> #endif >> >> >> So I thought that it is directly after the atomtype it belongs to. I >> thought that it is the same in the case with the water, where first the >> water definition is included and after that the restriction of the >> water. >> >> Or am I wrong? >> > > Well the #include statement shown here is different than the one you > showed > previously, which was wrong. Please always be sure you're providing > accurate > information - it wastes less time and avoids confusion. > >> I include the dummy atoms definition right after the ions. Or is this >> the >> wrong position? >> > > The position of #include statements in this context is irrelevant. You > can list > the [moleculetypes] in any order you like, but the relevant dependent > directives > must be contained appropriately and the order of the listing in > [molecules] must > match the coordinate file. Otherwise, it's fairly flexible. > > -Justin > >> >> 4935 4952 4950 4951 4 >> 4950 4954 4952 4953 4 >> 4954 4973 4972 4974 4 >> >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> >> ; Include water topology >> #include "amber03.ff/tip3p.itp" >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >> #endif >> >> ; Include topology for ions >> #include "amber03.ff/ions.itp" >> >> #include "amber03.ff/dum.itp" >> #ifdef POSRES >> #include "posre_memb.itp" >> #endif >> >> >> >> >>> >>>> So you mean that it is indeed important if I call it POSRES oder >>>> DPOSRES, >>>> right? >>>> >>> >>> Yes, syntax is crucial. The proper way to make use of #ifdef blocks is >>> described in the manual and in the link Mark posted. >>>
But when I only use "define = -POSRES" instead of "define = -DPOSRES" I get the warning: "WARNING 1 [file mdp file]: Malformed define option -POSRES" And also at the "http://www.gromacs.org/Documentation/How-tos/Position_Restraints"; site is written that in the mdp file there has to be "define = -DPOSRES " So is this the right way to write it in the mdp file. Although in the topology file which is generated by pdb2gmx stays "#ifdef POSRES"? Thank you >>> -Justin >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> 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 >>> * Only plain text messages are allowed! >>> * 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) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
