Hello, After running MD simulation using acemd3 software my waterbox is not staying cubic anymore. Water molecules are diffusing to very large space. Just to mention I prepared the input file using HTMD. Is it related to periodic boundary condition? Is it related to wrapping? Is my calculation wrong? How can I solve the problem?
Hey,
It's because of your periodic boundary conditions. Check the box size in your configuration file while applying PBC. Probably your box size is too large or your PBCs are not working properly.
Cheers,
Ali
Hey Musabbir! To me it doesn't look like you had a production run. It looks like you have started to equilibrate your system and didn't finish yet. How did you decide that your system was in equilibrium? I think you shall simulate longer and then you'll see the box again.
Hi Ali, Do you know how can I implement PBC in HTMD/ACEMD system? Thanks
Hi Inna Ermilova , longer equilibrate is not helping. I tried with ACEMD. However "barostat on" and "barostatpressure 1.01325" on production run is giving me cubic perfect waterbox.
What is your opinion or suggestion?
Thanks a lot.
Hi Musabbir! For how long time exactly did you equilibrate and how many atoms have you got in your system? Actually, these numbers matter, because the pressure does not say anything except that it is 1 atm.
It looks like there is an option for 'wrap' in ACEMD for the output. That should be turned on, otherwise the the waters will appear non cubic when they should be located within the periodic box.
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