Sorry I should mention it at the very beginning that I have a linear molecule and the angle is to be constrained at 180 degree. So what is the best way of constraining the angle for the linear molecule ?
On Tue, Jul 24, 2012 at 2:06 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 24/07/2012 6:07 PM, Broadbent, Richard wrote: >> >> An Angle constraint amounts to fixing a triangle. To do this you need to >> constrain the distances between all the atoms as you know the of the bonds >> 6064, 6063 and 6063, 6065 and the angle between the two bonds it is a >> trivial geometry problem calculate the length of the third side of the >> triangle (6064,6065). However, as you are attempting to hold these atoms >> in >> a straight line I would suggest that a type 2 virtual site might >> (depending >> on your system) be a better idea. > > > Indeed, a much better idea. > > Mark > > >> >> Richard >> >> >> On 24/07/2012 07:21, "tarak karmakar" <tarak20...@gmail.com> wrote: >> >>> Oh ! Thnaks >>> I saw that table, the angle_restrain option is there but not constraints >>> . >>> Anyway if suppose, I fix the distance between the two terminal atoms >>> of the molecule, the angle will eventually be fixed at a particular >>> given value. Is that the logic ? >>> Actually I searched for this problem so many times but didn't get >>> proper clue; in one of those mails I saw someone has dealt with some >>> dummy atoms. I could not able to digest that logic. >>> >>> On Tue, Jul 24, 2012 at 11:01 AM, Mark Abraham <mark.abra...@anu.edu.au> >>> wrote: >>>> >>>> On 24/07/2012 3:21 PM, tarak karmakar wrote: >>>>> >>>>> Dear All, >>>>> >>>>> >>>>> I am constraining one angle in my protein sample by incorporating " [ >>>>> constraints ]" block in topology file as >>>>> >>>>> >>>>> [ constraints ] >>>>> ; index1 index2 index3 funct angle >>>>> 6064 6063 6065 1 180.0 >>>>> >>>>> while doing that its showing the following error >>>>> >>>>> Program grompp, VERSION 4.5.5 >>>>> Source code file: topdirs.c, line: 174 >>>>> >>>>> Fatal error: >>>>> Invalid constraints type 6065 >>>>> For more information and tips for troubleshooting, please check the >>>>> GROMACS >>>>> website at http://www.gromacs.org/Documentation/Errors >>>> >>>> >>>> As you will see in table 5.6, this is not a valid option for >>>> [constraints] - >>>> you can only specify bonds. You will need to construct a triangle of >>>> bond >>>> constraints. >>>> >>>> Mark >>>> >>>> >>>>> >>>>> Then I rechecked the angle block, that specific angle is there in that >>>>> angle section, part of it as follows >>>>> 6039 6057 6058 1 >>>>> 6039 6057 6059 1 >>>>> 6058 6057 6059 1 >>>>> 6064 6063 6065 1 >>>>> 6067 6066 6068 1 >>>>> 6067 6066 6069 1 >>>>> 6068 6066 6069 1 >>>>> 6071 6070 6072 1 >>>>> 6071 6070 6073 1 >>>>> 6072 6070 6073 1 >>>>> >>>>> [ constraints ] >>>>> ; index1 index2 index3 funct angle >>>>> 6064 6063 6065 1 180.0 >>>>> >>>>> [ dihedrals ] >>>>> ; ai aj ak al funct c0 c1 >>>>> c2 c3 c4 >>>>> >>>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> 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 gmx-users-requ...@gromacs.org. >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
