On 2/26/13 6:37 PM, Divya Sunil wrote:
ok..thank you very much
The other thing I forgot to mention is that perhaps you can use a different box
shape. Dodecahedral and octahedral require a lot fewer water molecules than a
cubic box of equivalent periodic distance.
-Justin
On 26 February 2013 23:54, Justin Lemkul <[email protected]> wrote:
On 2/26/13 5:50 PM, Divya Sunil wrote:
Hello
I have a protein consists of 2303 atoms. I simulated it in water using
cubic box. As the protein has a long tail, the no. of water molecules to
fill the box is very high (132235). After simulation I converted the .gro
file to .pdb and in which I have seen that the atom number after 1 lakh is
again started to denote as 1 and also the molecule number after 9999 as 1.
So in this system there are 4 molecules that have number 1. Is this create
any problem during simulation/ before simulation? ( I noted this only
after
simulation and the system was not hanged) Also is it possible to remove
some water molecules manually after adding solvation to reduce the number
of atoms?
There is no problem during the simulation, and the fact that atom
numbering starts over is simply a limit of PDB format. Proper
representations can probably be obtained using other file formats.
Theoretically, there may be issues with creating index groups, but likely
only if dealing with water, and these issues can again likely be overcome
by choosing a different file format.
-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<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>
--
========================================
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
