Re: regarding umbrella sampling simulation

From: Nassar, Omneya (omnassar_at_UTMB.EDU)
Date: Fri Sep 14 2018 - 23:47:27 CDT

Hi San,

What is the total number of protein atoms in each box? Maybe you might have accidentally created a water box for the systems with ~80,000 atoms without including your protein in the system. If you used the VMD plugin GUI Solvate, the “Water Box Only” might have been checked without you noticing and now you only have water boxes with no protein in them.

Hope that helps and let me know what you find.

Thank you,


On Sep 14, 2018, at 11:17 PM, san kumar <<>> wrote:

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Dear NAMD users,

I am relatively new in molecular simulation field. I am using NAMD umbrella sampling tutorial to set up umbrella sampling simulation of my protein using NAMD. I solvated each window such that there was a minimum distance of 13 Å between any protein atom and a box side in all directions. The total number of water molecules in all windows is not the same. The total number of atoms in most of the windows is ~100,000 and in some windows, it is ~80,000.

So, is it necessary to solvate each window using same size of water box?

Any kind of advice/ suggestions will be deeply appreciated.

Thanks in advance,

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