Dear Carsten could you give me more information about your suggestions? I tried but probably I did not understand well what you meant.
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? 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? Thank you very much! Anna >----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 > > -- 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
