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?
> 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, > <[email protected]> wrote: >>> >>> >>> 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? 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