Hii
I am running MD simulations of water. First i have done the minimization, and then I have given the temperature of 300 by velocity command and then i have used the nve fix. It shows an error
as " bond atoms 46 47 missing on proc 0 at step 1248".
Please suggest a solution.
There are multiple possible reasons for this and thus there would be multiple possible solutions.
First you need to figure out what the reason is.
Possible reasons are lack of an equilibration period with a thermostat, unsuitable force field parameters or unsuitable simulation settings (e.g. too large a time step, or lack of a fix shake command).
You should change your thermo setting to output thermodynamic simulation info frequently, say every 10 steps and monitor temperature and potential energy. do they remain reasonable or are they changing a lot?
Visualizing your trajectory can also help to identify what is happening.
This is a commonly encountered error, so there are many previous discussions in the mailing list archive. I suggest you dig around and see what happened to others and how they dealt with it.
I have done the minimization in the separate MD simulation and it ran well… But when i have given the temeparature this error comes… Can i just increase the temperature slowly like first by 10 then by 100 etc…
Also will Shake command effect the minimization?
But the error doesn’t happen instantly but after over 1000 MD steps. That means that your minimization may be stuck in some local minimum and once the MD starts the system can reach configurations that were not previously accessible.
At any rate, how about you look into the list of things that I suggested to you first and learn more about what is going on rather than making me guess without sufficient information and thus increasing the chances massively that my guess is wrong. Then you may be spending much more time solving the wrong problem.
You cannot use fix shake with minimization.