RE: AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished

From: Ross Walker <ross.rosswalker.co.uk>
Date: Thu, 29 Mar 2007 21:33:37 -0700

Dear Pankaj,
 
The problem you are seeing is a function of your system essentially blowing
up. What happens is some atom has experienced a huge force and has shot off
a long distance to such an extent that the algorithm that resets the H
positions for SHAKE cannot successfully run and thus you see a shake error.
 
This is likely due to your initial structure being fairly strained and so
you will likely have to be much more gentle with it initially.
 
To find out where the problem is occuring you could try turning off shake,
setting the time step to 1fs and setting ntwx=1 and ntpr=1. Then run for a
few hundred steps until things start to go wrong, you'll likely see a huge
temperature. Then open the trajectory file in a visualization program and
you should be able to see where the problem originates. Then it may be a
simple fix in the initial structure.
 
I would also try with weaker restraints and remove them more slowly.
 
E.g. start by minimizing the whole system with no restraints. (maxcyc=1000,
ncyc=500)
 
Run 20ps heating from 0 to 100K at constant volume (use nmr restraints to
ramp the temperature and ntt=3, gamma_ln=2.0) with restraints on the solute
of 10.0 or so.
 
then heat the system up from 1000 to 300K gently over 80ps or so (use nmr
restraints to ramp the temperature and ntt=3, gamma_ln=2.0) with restraints
on the solute of 10.0 or so this time as constant pressure, then stick at
constant pressure as you equilibrate.
 
Next run for 100ps at 300K with the restraint for reduced to 1.0, then 100ps
with it at 0.1. Then remove the restraints entirely and continue your
equilibration.
 
This should hopefully work. If you still get problems then you will have to
inspect the starting structure more closely for overly stretched bonds,
atoms too close etc. If you still have problems you can try a longer period
of low temperature MD (100K or so) with a short time step say 0.5fs or less.
 
Good luck...
 
Ross
 
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|\oss Walker

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  _____

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Pankaj R. Daga
Sent: Thursday, March 29, 2007 20:59
To: amber.scripps.edu
Subject: AMBER: Sander error : Coordinate resetting (SHAKE) cannot be
accomplished


Hi Amber community,
 
Greetings. I am running equilibration of one quaternary system composed of
protein, DNA, Ligand and two Mg+2 ions. After minimization, as suggested by
Amber developers, I carried out equilibration with langevian thermostat,
without heating up the system, with harmonic constraints of 50.0 for solute.
 
In next step I removed the harmonic constraints and subjected it for
equilibration. But I am getting this error as follows. I have attached the
input files along with.
 
Could anyone please tell me, how can I solve the solution.
 
Regards
 
Pankaj
 
****************************************************************************
**********
 
p31_2777: p4_error: net_recv read: probable EOF on socket: 1
p30_2775: p4_error: net_recv read: probable EOF on socket: 1
p29_2773: p4_error: net_recv read: probable EOF on socket: 1
bm_list_2717: (42.125000) net_send: could not write to fd=5, errno = 9
bm_list_2717: p4_error: net_send write: -1
    p4_error: latest msg from perror: Bad file descriptor
p20_2755: p4_error: net_recv read: probable EOF on socket: 1
     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 3198 6542 6543
 
     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
[1] MPI Abort by user Aborting program !
[1] Aborting program!
p1_2718: p4_error: : 1
 
****************************************************************************
************
 
PanDa

 
===================================================================
If your ship doesn't come in, swim out to it.......Jonathan Winters
===================================================================
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
===================================================================




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Received on Sun Apr 01 2007 - 06:07:34 PDT
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