Hi okey, thank you!! > > > On 7/26/12 8:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hmm, okey. Thank you. >> So all in all what I did was correct and it should only minimize the >> hydrogen atoms and not the rest of the protein nor the membrane. Right? >> > > To sum up: > > 1. The Protein-H group does indeed contain only protein heavy atoms. > 2. Restraints do not guarantee that these atoms will not move, but they > disfavor > such motion. > 3. The initial block of topology you showed us: > > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > #ifdef POSRES > #include "posre_memb.itp" > #endif > > was wrong. > > 4. The later block of topology: > > ; 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 > > is syntactically correct and likely works as intended. > > 5. To invoke position restraints, one needs to prefix with -D, i.e. > -DPOSRES. > > -Justin > >> >>> Quite sure it's just different syntax in topology and mdp file. Compare >>> to >>> C; >>> #define POSRES // expressed as -DPOSRES in the mdp file >>> #ifdef POSRES // when working in the topology file >>> >>> // Linus >>> >>> On Thu, Jul 26, 2012 at 1:52 PM, >>> <reising...@rostlab.informatik.tu-muenchen.de> wrote: >>>>> >>>>> >>>>> On 7/26/12 7:06 AM, reising...@rostlab.informatik.tu-muenchen.de >>>>> wrote: >>>>>>> >>>>>>> >>>>>>> On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de >>>>>>> wrote: >>>>>>>>> On 26/07/2012 6:47 PM, >>>>>>>>> reising...@rostlab.informatik.tu-muenchen.de >>>>>>>>> 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 gmx-users@gromacs.org >>>>>>> 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 gmx-users-requ...@gromacs.org. >>>>>>> * 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 gmx-users@gromacs.org >>>>> 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 gmx-users-requ...@gromacs.org. >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>> >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> 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 gmx-users-requ...@gromacs.org. >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> * 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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