| 1:04:58 PM PST - Tue, Nov 26th 2013 |
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Hi Jingbo,
From my experience, This error comes from 2 reasons. The first one is the dimension box is to tight as suggested by TBS. Yes, you can increase dimension box from the restart file directly or recreate the new restart file. There is no rule about how much we should increase the box. In my case, I tried 0.2 nm to each dimension and that did fix my problem. Please keep in mind that increasing too much will cause the water box not rectangular any more. In case you use PBC, I'm not sure this will affect the result or not so you need to be aware of that. If this cannot solve the problem, there is likely to be a chance that there is something bad happen to the solvent. Have you ever extracted the pdb file from the restart file to see what might go wrong for water molecules? From my experience, I always spot some waters clumping together (getting too close). From time to time, this can be fixed if you run constant energy MD or optimize the structure. This may drive those clumping waters apart but unfortunately sometimes it does not help either.
My another question is how long do you equilibrate you system at once. If you equilibrate the system for a long time at once (e.g. > 10 ps), there is likely to be a chance that waters will be clumping together. This sounds like a bug in MD module as I talked to Marat. My advice is to equilibrate the system with shorter number of steps (5 ps or 5000 steps) at the time. For example, you want to equilibrate the system for 20 ps, you better do it for 5 ps 4 times rather than doing it 20 ps at once. So far, this seems to fix the problem for clumping waters, one source of 'Deviation too large for solvent'.
Hope this might help fix your problem. I also had a hard time figuring out how to completely get rid of this problem too.
Quote:Wjb0920 Nov 26th 9:01 amHi,
I encounter the same problem and searching the solution. I am appreciated if you can share me with your experience.
Did you increase the box dimension directly in the rst file? I want to know how long the box dimension you increased to make it go through the computation. In my simulation, I change the box dimension from 8 angstrom to 8.3, but still error. So the question is how long we can increase?
Thanks for your time.
Best,
Jingbo |
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