> > > 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? 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? I include the dummy atoms definition right after the ions. Or is this the wrong position? 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. > > -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 > -- 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
