[gmx-users] Number of atoms is very high
jalemkul at vt.edu
Wed Feb 27 00:40:01 CET 2013
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.
> On 26 February 2013 23:54, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 2/26/13 5:50 PM, Divya Sunil wrote:
>>> 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
>>> 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 A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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