Hi
look this archive
http://archive.ambermd.org/201004/0173.html
try time step 1fs
best wish
asaminew
On Thu, May 8, 2014 at 12:04 PM, Valentina Romano <
valentina.romano.unibas.ch> wrote:
> Dear Amber users
>
> I want to run a MD (heating fro 0 to 300K) with restraints on the solute
> (solute = protein-ligand complex).
>
> First of all, I minimized the system in 2 steps.
> 1) only solute restrained
> 2) all atoms free
> The input file for the 2nd step is:
>
> &cntrl
> imin=1,
> maxcyc=10000,
> ncyc=2500,
> ntb=1,
> igb=0,
> cut=12
> /
> Then I used the minimized structure as input for the MD heating stage.
>
> The MD was immediately stopped with the following error:
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -113244.2583 EKtot = 0.0000 EPtot =
> -113244.2583
> BOND = 140.4824 ANGLE = 683.5019 DIHED =
> 2272.1178
> 1-4 NB = 785.8019 1-4 EEL = 8760.7170 VDWAALS =
> 17150.2089
> EELEC = -143037.0883 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.1423E-03
>
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 1; vmax = 50.5448
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 1 1924 3839 3846
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> I think the error is related to the minimized structure I am using as
> input.
> Is there a way to check if the minimization went well (e.g.: an easy way
> to plot the total energy vs time steps)?
> How to check if it necessary minimize for a longer or shorter time?
>
> The last step of the minimization is the following:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 10000 -1.0588E+05 6.6968E-01 7.0286E+01 N9 3834
>
> BOND = 7509.5321 ANGLE = 683.5019 DIHED =
> 2272.1178
> VDWAALS = 17150.2089 EEL = -143037.0880 HBOND =
> 0.0000
> 1-4 VDW = 785.8019 1-4 EEL = 8760.7170 RESTRAINT =
> 0.0000
>
> While the enrgy at the step 0 of the MD is:
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -113244.2583 EKtot = 0.0000 EPtot =
> -113244.2583
>
> Could the difference in the energy values had influenced the error I got?
> If yes, I can solve it?
>
> Thank you
> Valentina
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB
> Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Asaminew H. Aytenfisu, Grad Student
David Mathews' group
Department of Biochemistry and Biophysics
University of Rochester Medical Center
Office: 3-8807
601 Elmwood Avenue, Box 712
Rochester, NY 14642
(585) 275-1748
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Received on Thu May 08 2014 - 09:30:05 PDT
