Hi Anna, On Jul 26, 2013, at 11:17 AM, battis...@libero.it wrote:
> 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 I think you do not need orientation restraints at all, just enforced rotation. > > 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? Yes, the rotation vector v you provide in the mdp file as rot_vec0, and u as rot_pivot0. It depends a bit on the rotation potential type you choose, for some of the potentials (the pivot-free ones) you do not have to provide a u vector, since it is calculated on the fly as the center of positions or as the center of mass (depending on whether you choose mass-weighting or not with the rot_massw0 parameter). If you have more than one protein that you want to constrain the rotation for, set rot_ngroups to a value larger than 1 and provide values for each group in rot_vec0, rot_vec1, and so on. > > 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? Yes, and you have to choose a spring constant (k, or rot_k0) that determines how close your protein stays at the given angle, i.e. how large you allow the fluctuations about the angle to be. Good luck! Carsten > > > 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 >> >> > > -- 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. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists