Hello Sir, Thanks for your reply sir. I will check to it.
With regards M. Kavyashree On Mon, May 30, 2011 at 4:59 PM, Tsjerk Wassenaar <[email protected]> wrote: > Hi Kavya, > > There is no way to correct for such things afterwards. But I would > guess it's not much of a problem in your case. If a situation with a > short distance is only transient, it is unlikely to affect the > simulation. On the other hand, you may have secondary, indirect > effects due to water ordering. Whether that is problematic in your > case is something you'll have to assess yourself. > > Cheers, > > Tsjerk > > On Mon, May 30, 2011 at 12:24 PM, Kavyashree M <[email protected]> wrote: > > Hello Sir, > > > > The difference between the rcolumb (1.4nm) and minimum image distance > > that was obtained between two hydrogen HZ2 and HZ3 atoms of 2 lysine > > residues (1.39714nm) is 0.00286nm = 0.0286Ang, > > Since this distance is smaller than bond distance between hydrogen and > > nitrogen which is ~1.0Ang, So will this effect the results of the > > simulations? > > Kindly let me know whether I need to redo the simulation again? or is > there > > any way to correct this or can it be ignored? > > > > Thanking you > > With regards > > M. Kavyashree > > > > > > On Mon, May 30, 2011 at 10:36 AM, Kavyashree M <[email protected]> > wrote: > >> > >> Hello sir, > >> > >> I had used a dodecahedron cell for simulation. I have run > >> the simulation for 100ns, did you man I have to restart the > >> simulation again? > >> > >> Thanking you > >> Kavya > >> > >> On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar <[email protected]> > >> wrote: > >>> > >>> Hi Kavya, > >>> > >>> > "shortest periodic distance is 1.39714 (nm) at time 21824 (ps), > >>> > between atoms 2062 and 3688" > >>> > where 2062 is a protein atom and 21824 is a water molecule. > >>> > >>> 21824 is the time in ps at which the two atoms indicated, 2062 and > >>> 3688, are at the short distance given. You can dump the frame with > >>> trjconv and have a look. Probably your molecule stretched, or you > >>> solvated in a rectangular box and the protein rotated. In the first > >>> case, set a larger distance, in the second, use a rhombic > >>> dodecahedron. > >>> > >>> Cheers, > >>> > >>> Tsjerk > >>> > >>> > >>> -- > >>> Tsjerk A. Wassenaar, Ph.D. > >>> > >>> post-doctoral researcher > >>> Molecular Dynamics Group > >>> * Groningen Institute for Biomolecular Research and Biotechnology > >>> * Zernike Institute for Advanced Materials > >>> University of Groningen > >>> The Netherlands > >>> -- > >>> 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 > >> > > > > > > -- > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- > 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 >
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