Re: residue based coarse-grained simulation

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Tue Nov 09 2010 - 09:51:03 CST

Hi Demet,

Have you made sure that your system is well minimized before starting dynamics? Have you tried slowly heating the system to your desired temperature, or do you just initialize your system at your target temp? Have you tried a smaller time step (in your email you say 'increasing time steps', but I'm not sure if this was a typo on your part)? Does your system blow up immediately in the first couple of steps? Which atoms are moving too fast? Have you looked at the area that is blowing up for bad contacts in your starting structure? Are you sure you don't have any strange bonds in your psf file? Have you looked at all of the issue listed in the troubleshooting wiki about 'atoms moving too fast'? (some which I list above):
http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting

There are obviously a lot of things to check, but answering these questions should be a decent list of things to ask while debugging what's going on.

Best wishes,
Josh

On Nov 9, 2010, at 8:03 AM, Demet Akten wrote:

> Dear All,
>
> We try to simulate a residue based coarse-grained simulation of a protein+lipid+water+ions at constant NPT. We tried different protocols for simulation, such as putting constraints on protein, increasing time steps, increasing the periodic box, etc. Unfortunately, we cannot prevent some atoms from moving too fast. Can you give us any suggestion on how to proceed with the simulation protocol?
>
> Thanks,
>
> Demet
>

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