Dear Ross,
Thanks indeed for your reply. This is the last step of the minimization
###########################################################
NSTEP ENERGY RMS GMAX NAME NUMBER
2000 -2.0441E+05 9.3899E-01 1.3212E+02 SG 2716
BOND = 13916.4330 ANGLE = 2155.3700 DIHED =
6633.1822
VDWAALS = 25899.3282 EEL = -288977.3753 HBOND =
0.0000
1-4 VDW = 2482.2353 1-4 EEL = 33479.2778 RESTRAINT =
0.0000
#################################################################
And this is the 1st few steps of the md:
#################################################################
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -217925.3004 EKtot = 0.0000 EPtot = -
217925.3004
BOND = 402.6816 ANGLE = 2155.3700 DIHED =
6633.1822
1-4 NB = 2482.2353 1-4 EEL = 33479.2778 VDWAALS =
25899.3282
EELEC = -288977.3754 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.9127E-04
------------------------------------------------------------------------------
NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 68534.32 PRESS =
0.0
Etot = 7845184.6709 EKtot = 8063109.9713 EPtot = -
217925.3004
BOND = 402.6816 ANGLE = 2155.3700 DIHED =
6633.1822
1-4 NB = 2482.2353 1-4 EEL = 33479.2778 VDWAALS =
25899.3282
EELEC = -288977.3754 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.9127E-04
------------------------------------------------------------------------------
vlimit exceeded for step 1 ; vmax = 76.6208829776301
NSTEP = 2 TIME(PS) = 0.000 TEMP(K) = 70569.85 PRESS =
0.0
Etot = 8111878.8687 EKtot = 8302592.0525 EPtot = -
190713.1837
BOND = 404.0291 ANGLE = 2152.9940 DIHED =
6632.7920
1-4 NB = 2481.8376 1-4 EEL = 33476.3115 VDWAALS =
25973.9272
EELEC = -261835.8866 EHBOND = 0.0000 RESTRAINT =
0.8114
EAMBER (non-restraint) = -190713.9951
Ewald error estimate: 0.1001E-03
------------------------------------------------------------------------------
NSTEP = 3 TIME(PS) = 0.000 TEMP(K) = 8042.59 PRESS =
0.0
Etot = 755499.6883 EKtot = 946215.9061 EPtot = -
190716.2178
BOND = 404.0192 ANGLE = 2152.9879 DIHED =
6632.7893
1-4 NB = 2481.8348 1-4 EEL = 33476.3243 VDWAALS =
26028.0885
EELEC = -261893.0728 EHBOND = 0.0000 RESTRAINT =
0.8109
EAMBER (non-restraint) = -190717.0287
Ewald error estimate: 0.9622E-04
##################################################################
As can be seen from the results of md, the temperature jumped from 0K at 0
step to 68534.32K at step 1, which shouldn't happen at all and caused the
job terminate. Can i ask what might be the causes of this big temperature
jump?
Thanks indeed.
Best regards,
Rachel
On 11/22/06, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> Dear Rachel,
>
> Seeing shake failure is a function of deeper problems with your system and
> is not an issue with using shake. If you turn off shake and run the
> simulation your simulation will run for longer and then die.
>
> The issue is most likely that you have a very bad/strained starting
> structure that minimization could not clean up. Unfortunately you don't give
> the energies for the first step of your MD or from the end of your
> minimization so it is hard to see where the problem is coming from. Often
> though these problems arise because you have 2 atoms sitting on top of each
> other.
>
> You can try the check command in leap. You should also look at your
> minimisation and see which atom has the largest force on it - printed on the
> NSTEP line. This will give you a clue where to look. You can also, if you
> want to see what is going wrong, set the time step very short, say 0.1fs(dt=
> 0.0001) and also set ntwx=1 and turn off shake. Then run for about 50
> steps or so and then open the trajectory file in a viewer such as vmd and
> you should be able to watch your system blowing up and see from where the
> problem originates.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Rachel
> *Sent:* Wednesday, November 22, 2006 03:39
> *To:* amber
> *Subject:* AMBER: SHAKE problem after minimization
>
>
> Dear all,
>
> I have a problme with SHAKE after minimization, when I started to run md,
> this is the error message i got:
>
>
> ------------------------------------------------------------------------------------------------------------------
>
> Coordinate resetting (SHAKE) was not accomplished
> within 3000 iterations
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> ----------------------------------------------------------------------------------------------------------------
>
>
> And the following are the scripts i used to run minimization and md:
>
>
> --------------------------------------------------------------------------------------------------------------
>
> initial minimisation whole system
> &cntrl
> imin = 1,
> maxcyc = 5000,
> ncyc = 2000,
> ntb = 1,
> ntr = 0,
> cut = 10
> /
> --------------------------------------------------------------------------------------------------------------
>
>
>
> -------------------------------------------------------------------------------------------------------------
>
> res on the protein with 0.5fs timestep
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 10,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 30000, dt = 0.0005,
> ntpr = 100, ntwx = 100, ntwr = 500
> /
> Keep the protein fixed with weak restraints
> 10.0
> RES 1 791
> END
> END
>
>
> ---------------------------------------------------------------------------------------------------------------------
>
> I have tried to use even smaller timestep such as 0.3fs or even 0.1fs, but
> still i had same problem, and when i used very small timestep such as
> 0.1fs, i will have error messages ' vlimit exceeded for step 1 ; vmax =
> 76.6082699232639' as well before it complained about the SHAKE problem.
>
> Can anyone suggest what might be the causes of this SHAKE failure please?
> thanks a lot in advance!
>
> Best regards,
>
> Rachel
>
>
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Received on Wed Nov 22 2006 - 23:01:53 PST
