RE: AMBER: SHAKE in md with partial solvation

From: Ross Walker <>
Date: Mon, 6 Jun 2005 10:12:20 -0700

Dear Ye,

> NSTEP = 4500 TIME(PS) = 13.000 TEMP(K) =
> 306.89 PRESS = 0.0
> Etot = -2812.1921 EKtot = 1628.5984 EPtot
> = -4440.7905
> BOND = 362.2453 ANGLE = 1021.4029 DIHED
> = 1348.8158
> 1-4 NB = 441.4590 1-4 EEL = 5960.7192 VDWAALS
> = -434.6513
> EELEC = -13140.7814 EHBOND = 0.0000 RESTRAINT
> = 0.0000
> --------------------------------------------------------------
> ----------------
> vlimit exceeded for step 4580 ; vmax = 44.619679589066607
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 638 1406 1405
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> Then I checked the heated structure, and found that those
> residues which should be kept fixed in heat-up procedure also
> have their coordinates changed. The constant temperature md
> simulation died because some hydrogens moved far away from
> atoms they connect to.
> Is there anything wrong with my input files in the
> attachment? Or how to keep those faraway residues fixed
> during md simulation?

Something is very wrong with your structure leading to it blowing up.
Chances are some hydrogens are flying off too far, so far in fact that the
SHAKE algorithm cannot correct their positions. You are going to have to
find out what is wrong with your system. I would start by switching off
shake and setting the time step to either 1fs or 0.5fs. Then run the
simulation with ntwx=1 so that it records every frame to the mdcrd file. You
can then closely watch it in something like VMD where you may be able to see
the origin of the "blow up".

You may find that belly is the cause of your problems. If you are fixing the
residues in real high energy configurations it may be putting a huge strain
on the rest of your system. This is especially true since you fix a lot of
residues even during the minimisation. Try minimising without belly and then
fix the residues, they shouldn't move far during the minimisation so it
should cause you problems.

You may need to heat your system more slowly using weight restraints.

Another thing I notice is that you are using a solvent cap but you have not
restraint energy. Have you applied all the latest bug fixes? Specifically
bugfix.33, 40 and 43?

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Mon Jun 06 2005 - 18:53:00 PDT
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