> Hello again, > > I centered it and then did the calculation again for minimum image > distance > but still it showed the same graph as without centering. I tried > visualising > it > using vmd but could not see any such clashes. since I am new to vmd > I do not know whether it is possible to calculate such clashes if at all > in vmd? I am using dodecahedron box. can it be visualised as it is in vmd? >
In VMD go to graphics then representations and select periodic. In periodic by clicking on +/- of each axis you can check if your protein bumps into itself. Best, Sarath > Thank you > With regards > Kavya > > On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M <[email protected]> wrote: > >> Thanks. >> >> >> On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul <[email protected]> >> wrote: >> >>> >>> >>> Kavyashree M wrote: >>> >>>> Dear users, >>>> >>>> I was trying to simulate a protein dimer covalently bond with >>>> a disulphide bond (230+230 aa long). I used usual protocol >>>> as used for simulation of a monomeric protein, using gromacs- >>>> 4.5.3, dodecahedron box, tip4p water model and protein to >>>> box distance of 1 (-d in editconf). In the middle of the simulation >>>> when i checked for minimum image violation there was huge >>>> clashes. I am extremely sorry I have been asking regarding this >>>> many times but in this it is a dimer and I am not sure what mistake >>>> I have done because this happened while simulating another dimer >>>> also though not sever. Hence I seek some guidance from this >>>> community regarding the problem. I attach the graph herewith. >>>> Kindly help. Let me know if I need to give any other information. >>>> >>>> >>> Please see my post from yesterday for a more detailed reply to this >>> exact >>> same type of question. I am beginning to suspect there's a problem >>> with >>> g_mindist, but I have no solid evidence for that claim, just a hunch. >>> It >>> looks like your protein crosses a periodic boundary and that messes up >>> the >>> calculation. Please center the protein in the box with trjconv -center >>> and >>> re-analyze to see if there are any differences. >>> >>> -Justin >>> >>> -- >>> ==============================**========== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> >>> ==============================**========== >>> -- >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >> >> > -- > 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 -------------------- Sarath Chandra Dantu Computational Biomolecular Chemistry Max Planck Institute of Biophysical Chemistry Am Fassberg 11, Gottingen 37077 Germany Email: [email protected] Tel: ++49-551-201-2320 Fax: ++49-551-201-2302 -- 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
