AMBER Archive (2005)

Subject: Re: AMBER: SHAKE in md with partial solvation

From: Germán Sciaini (gsciaini_at_qi.fcen.uba.ar)
Date: Mon Jun 06 2005 - 05:34:09 CDT

The time step is high, try with 1ps or 0.5 ps....

Good luck....
G.

At 03:30 p.m. 05/06/2005, you wrote:

>Dear amber users£¬
>
>I met a problem with SHAKE in md simulation of a partially solvated
>system. 20A TIP3P water cap is added to the peptide, around the
>catalytic site. All residues, including waters, that are more than 15A
>away from the catalytic site are not allowed to move. The system is first
>minimized in 2000 steps, followed by 2000 steps heat-up with step size
>2fs. Then the constant temperature md simulation is performed. SHAKE is
>implemented in both heat-up and constant temperature md simulation. But an
>error message says:
>
> 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?
>¡¡¡¡¡¡¡¡¡¡¡¡
>
>Best regards,
>
>Ye Mei
>ymei_at_itcc.nju.edu.cn
>Institute of Theoretical and Computational Chemistry
>Key Laboratory of Mesoscopic Chemistry
>School of Chemistry and Chemical Engineering
>Nanjing University
>Nanjing 210093
>P.R.China
>2005-06-05
>
>
>
>
>
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