Mark, This sounds like I use very small forces but expect reasonable effect. But I've applied different forces with step-by-step increasing of force constants ( from very softest comparable with the thermal motion ( 0.1 kj mol nm-2) to relatively hight (10). As the consequence I've observed effect of application of that harmonic constraints wich I've defined in the r0 and r1 range but in some case ( where forses were were hight I've seen perturbation of my structures) and when constraints were low ( in accordance to my literature) I've not seen desired effect like the selection of the constraints was wrong ( but actually all restraints were applied on the correct possitions). This was seen by measurement of the distances between atom pairs wich were contrained. Eg If I define this distances in the 0.1<Rij<0.4 ( r0=0,1 r1=0,4 for this instance) range the real distance between i and j atoms in the simulated structure was lower or higher of the defined range.
By the way I've found that besides such harmonic restraining also I can apply more rigid holo restraints from specified value. Could you tell me where I could find information of the application of such restraints in the topology of my protein? As I understood this could be done by means of editing of the bond enty in topology but what exactly specified type should I applied on the restried atoms? Thank for help again, James 22 марта 2012 г. 17:32 пользователь Mark Abraham <mark.abra...@anu.edu.au>написал: > If there's a car at the bottom of one valley in the Alps, and you think it > should be two valleys over, and you pull it with a trained cat... it's not > going to move much. How big an animal you need depends on the geography. > There need not even be a reasonable route for you to take, if the target > valley is effectively on Mars. > > Mark > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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