Thanks Justin & Chaban. Even I did the simulation for 3 ns and it worked well. Now the issue in my case is , while I was not imposing the M-N constraints, the metal was rattling around (little bit) and the histidine residues were moving back and forth (elongation of M-Nhis length). So I employed constraints to keep them in peace. But I'm bit worried about the dynamics of the entire protein. I'm not sure how accurate results these will produce if I impose these sorts of approximations. Any idea ? Any reference where people have followed the same ?
Thanks Tarak On Fri, Oct 12, 2012 at 8:26 PM, Justin Lemkul <[email protected]> wrote: > > > On 10/12/12 10:39 AM, Dr. Vitaly Chaban wrote: >>> >>> >>> On 10/12/12 2:42 AM, tarak karmakar wrote: >>>> >>>> Dear ALL, >>>> >>>> In my protein I need to constraint the length between the Metal and >>>> the N of Histidine residues. In the .rtp file I didn't specify this >>>> Mn-N connectivity; these are more or less coordinate bonds. So to do >>>> that I specified the Mn, N-atom indices and the corresponding lengths >>>> in the topology file, part of it is given below >>>> >>>> >>>> [ constraints ] >>>> ; index1 index2 funct length(nm) >>>> 6062 6063 1 0.11490000000 >>>> 6062 6064 1 0.11490000000 >>>> 6060 4309 1 0.21000000000 >>>> 6060 4268 1 0.22700000000 >>>> 6060 4979 1 0.22600000000 >>>> >>>> >>>> In the .mdp file I have included the following lines >>>> >>>> >>>> constraints = h-bonds ; covalent h-bonds constraints >>>> constraint_algorithm = LINCS ; LINear Constraint Solver >>>> continuation = yes ; apply constraints to the >>>> start configuration >>>> lincs_order = 4 ; highest order in the >>>> expansion of the contraint coupling matrix >>>> lincs_iter = 1 ; number of iterations to >>>> correct for rotational lengthening >>>> lincs_warnangle = 30 ; [degrees] maximum angle that >>>> a bond can rotate before LINCS will complain >>>> >>>> >>>> [ I followed the above mentioned protocol and I see Mn-N distances are >>>> not changing during the simulation, so served my purpose.] >>>> >>>> So for all sorts of specified constraints (H-covalent bonds, Mn-N >>>> coordinate bonds), MD will make use of LINCS algorithm !! . But my >>>> query is about whether LINCS will be equally applicable as that of for >>>> covalent bonds in constraining Mn-N distances where the real(?) >>>> bonds(connectivity) don't exist !! >> >> >> Introducing constraints between non-covalently bound sites may (and >> often does in practice) result in the instability of your system and >> may require smaller time-step. >> >> Personally, I would introduce morse potential with a weak force >> constant for the same task . >> > > For what it's worth, I've employed a similar setup as the OP and it worked > quite well, though there are probably several ways to address this issue. I > can think of at least four. > > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tarak -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
