Dear Carsten, thank you very much for your support!
At the beginning I did not follow your indications correctly but now, using the orientation restraints and the indication in the paper Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS Kutzner C, Czub J, and Grubmüller H J. Chem Theory and Comp. 7: 1381-1393 (2011) I believe I made it. Just few questions to be sure, if I can: how the vector v ( namely the axis rotation defined in the paper) is defined? giving a (large) number of atoms as rotation group, I suppose that the vector u identify the center of mass of the group, and in this point the v vector defines the direction that one gives with the rot_vec entry in mdp file. Is it correct? I suppose that in order to just keep the direction of the v axis during the dynamics, my choise have to be rote_rate=0, is it correct? Thanks again, Anna >----Messaggio originale---- >Da: ckut...@gwdg.de >Data: 25/07/2013 11.12 >A: "battis...@libero.it"<battis...@libero.it> >Cc: "Discussion list for GROMACS users"<gmx-users@gromacs.org> >Ogg: Re: [gmx-users] Rotation Constraints - PMF - external potential > >On Jul 24, 2013, at 5:53 PM, battis...@libero.it wrote: > >> Dear Carsten >> >> could you give me more information about your suggestions? >> I tried but probably I did not understand well what you meant. >Hi Anna, > >I suggested to use the enforced rotation module of Gromacs 4.6 >to restrain the orientation of your molecule(s). If you want to >use the orientation restraints module instead, I am afraid I >can not help you much with that, maybe someone else on this list? > >> In order to avoid the rotation of the structure A and of the structure B, I >> have defined into the index file a group A_B that contains A+B and I have >> setted in the mdp file the following parameters: >> >> ; Orientation restraints: No or Yes >> orire = yes >> ; Orientation restraints force constant and tau for time averaging >> orire-fc = 500 >> orire-tau = 100 >> orire-fitgrp = A_B >> ; Output frequency for trace(SD) and S to energy file >> nstorireout = 100 >> >> As I have synthetically described in the first post , the structures A and B >> (characterized by a cylindrical shape) are defined by a number of 32 unit- >> structures that I call s. >> >> Into the itp is defined the topology for the s structure, and so in order to >> put an orientation restraints between atoms that are not included into the same >> itp file, >> I cannot put into the topology a section like that described into the manual >> 4.6.2 pag. 92 namely, [ orientation_restraints ], could I ? >> >> Could you tell me How I can fix the orientation of the systems A and B? >Using the enforced rotation module you would choose an index group and an axis >for each group that you want to fix the orientation, set the rotation angle to >zero and choose an appropriate force constant. Appropriate potential functions >would be the pivot-free ones if I understand your setting correctly. >> >> I don't understand the manual's explanation about the orire-fitgrp: >> (fit group for orientation restraining. This group of atoms is used to >> determine the rotation >> R of the system with respect to the reference orientation. The reference >> orientation is the >> starting conformation of the first subsystem. For a protein, backbone is a >> reasonable choice) >> >> How one have to give the group? using an index file or defining the group in >> the topology? >This is the "orire-fitgrp = A_B" mdp file setting that you made. > >Best, > Carsten >> >> >>> ----Messaggio originale---- >>> Da: ckut...@gwdg.de >>> Data: 23/07/2013 13.09 >>> A: "battis...@libero.it"<battis...@libero.it>, "Discussion list for GROMACS >> users"<gmx-users@gromacs.org> >>> Ogg: Re: [gmx-users] Rotation Constraints - PMF >>> >>> Hi Anna, >>> >>> please have a look at the Enforced Rotation Section in the Gromacs 4.6 >> manual. >>> You can restrain the angle of rotation about an axis by setting the rotation >> rate >>> to zero. There is also a 4.5 add-on available with rotational restraints in >>> the Gromacs git repository (branch "rotation"). For more info you may want to >>> look at this page: >>> >>> http://www.mpibpc.mpg.de/grubmueller/rotation >>> >>> Best, >>> Carsten >>> >>> >>> On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: >>> >>>> Dear user and expert, >>>> I'd like ask you a suggestion about a problem that I will try present you >> schematically. >>>> I have got a structure "s" and I have generated the topolgy file itp for it. >> A number of separate "s" in turn generate a complex structure A, that is >> characterized by a cylindrical shape. >>>> Now, I constructed a system with two cylindrical structures, A and B (in >> total made by 64 "s" structures), and I'd like make an Umbrella Sampling >> calculation in order to study the PMF varying the distance between A and B. >>>> >>>> My problem is that I'd like fix the orientation of the axis of each >> structure A and B long the z axis, during the dynamics. >>>> So I need to put a force into the system or a constrain, such that when the >> axis of A or B rotates respect to z axis, the force puts back the axis of the >> structure in the z direction. >>>> >>>> It this possible? If it is so, could you tell me how to do that? >>>> Than you very much, >>>> Anna >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> * 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 >>> >>> >>> -- >>> Dr. Carsten Kutzner >>> Max Planck Institute for Biophysical Chemistry >>> Theoretical and Computational Biophysics >>> Am Fassberg 11, 37077 Goettingen, Germany >>> Tel. +49-551-2012313, Fax: +49-551-2012302 >>> http://www.mpibpc.mpg.de/grubmueller/kutzner >>> http://www.mpibpc.mpg.de/grubmueller/sppexa >>> >>> >> >> > > >-- >Dr. Carsten Kutzner >Max Planck Institute for Biophysical Chemistry >Theoretical and Computational Biophysics >Am Fassberg 11, 37077 Goettingen, Germany >Tel. +49-551-2012313, Fax: +49-551-2012302 >http://www.mpibpc.mpg.de/grubmueller/kutzner >http://www.mpibpc.mpg.de/grubmueller/sppexa > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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. 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