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Yes, I am concerned about Temp and Energy values. Every 1000 steps (NTRFRQ) the T dramatically drops. You can see this in the last post. How can I fix this? As I stated before I've tried using a large value than I got the 'flying ice-cube' kind of behavior. I also tried using smaller values (5, 50, 100) then the simulation crashed. Also, this only happens when I run it on parallel. The results from truly serial charmm does not do it, i.e. T does not change when NTRFRQ acts.

Last edited by TGK; 10/28/09 08:18 PM.
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The energy tolerance errors with a smaller NTRFRQ may indicate that the model was not adequately minimized prior to assigning initial velocities. Be sure to minimize with PBC, Ewald, etc., exactly as will be used for the simulation. Then try heating from 198 K over 100 ps or more, and use a smaller NTRFRQ value.

Finally, it should be noted that there can be and have been bugs in CHARMM; some older versions of CHARMM had a couple parallel bugs that might cause this.


Rick Venable
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Try CWR (crawl-walk-run), something like this (and look at the examples in the Script Archive!):
One dipeptide in a box of waters (and do delete waters that overlap with the peptide); we skip the waters-only step for now.
setup PBC

shake bonh
minimize sd nstep 500 atom cdie cutnb 14 ctofnb 12 fshift vshift
minimize abnr nstep 500

dynamics start nstep 50000 timestep 0.002 inbfrq -1 imgfrq -1 -
firstt 198 finalt 298 temin 10 ihtfrq 1000 -
iunwrite ... iuncrd ...

When this works OK, add a few more dipeptides and try again.
When this works OK, add the PME stuff (if you strongly feel a need for this).


Lennart Nilsson
Karolinska Institutet
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Okay thank you. The same thing happens with a well equilibrated waterbox (with no peptides).

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The only possible answer with the information you have given is that you have made a mistake. Period. The solution is very simple: Fix the mistake.

I do not understand how a well equilibrated waterbox can suddenly be misbehaved. What do you do differently from the equilibration part?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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