Nancy Deng wrote:
Hi Mark,
Thanks for the quick response and the funny story :)
I indeed want to collect the possible comformation of a certain small
molecule (a little car made of 35 atoms around 15 A in length) by MD.
Since obvious to my understanding that in vacume or in water
environment, the small molecule could behave quite different (i really
want to see this happens :). So, my goal is to compare the difference of
the two MD trajectories ( for example 5 ns or even longer) of the small
molecule by Gromacs. But i am stuck even at the very beginning which i
could never reach either New York or Detroit :(
In the case of no-water simulation, the box without water was generated
by "editconf" but not followed by "genbox" to avoid water filling in.
The other box was consequently generated by "genbox" to contain 370 SPC
water molecules. During the equilibration stage, the water particles
seems prefer to roam away from the originally centered small molecule,
which i guess the reason to increase the overall size of the box...
Not sure whether this provides some useful input to help me out of the
trouble :)
We need to know the kind of simulation you're attempting (ensemble,
etc.), the size box you're using and its density, your equilibration
regime, whether you got any warnings from grompp, and probably other
stuff I can't think of now, in order to tell where you're breaking things.
Have you tried the tutorial material?
Mark
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