[gmx-users] peptide out of box
operin at pasteur.fr
Tue Mar 13 08:34:26 CET 2007
4ns becomes a long dynamic simulation. Sometimes during such a
simulation, the system moves such a way that it "seems" to get out of
the water box.
In order to prevent this phenomen, you can use one parameter normally
used during a simulation in vaccum:
nstcomm = 500 ;
You can add this line to your mdp file before the grompp step. This is
the frequency for center of mass motion removal.
About the 2.2nm: if it is the real size of your box, I agree with the
answer of Mark, the box is probably to short. But if it's your "-d"
parameter for editconf, it is largely sufficient.
Mark Abraham a écrit :
> Rakesh Mishra wrote:
>> When I run simulations on a 42 residue peptide with a box size of 2.2
>> nm , I find that after 4 ns , the peptide comes out of the box . Is
>> this a problem as far as the accuracy of the simulation results are
>> concerned. Do the periodic conditions account for such cases? If not
>> , is there any suggestion as to how I may salvage my data without
>> having to start all over again .
> The peptide can't "come out of the box" - the system is periodic. The
> numbers in the trajectory file can be such that your visualization
> software will render an image that looks like the peptide comes out of
> the box, however. Look at the man page for trjconv and choose an
> option appropriate for your situation and use that on the trajectory
> before visualizing.
> By the way, a 42 residue peptide is almost certainly too large for
> such a box, even if it is a compact peptide. There are guaranteed to
> be many water molecules (or even all of them) that are having
> non-bonded interactions with two images, which is unphysical.
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