[gmx-users] Minimum periodic distance
hmkvsri at gmail.com
Mon May 30 12:24:32 CEST 2011
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
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?
On Mon, May 30, 2011 at 10:36 AM, Kavyashree M <hmkvsri at gmail.com> 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
> On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>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
>> 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 gmx-users at gromacs.org
>> 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users