AMBER Archive (2006)

Subject: Re: AMBER: SHAKE problem after minimization

From: Rachel (comeonsos_at_googlemail.com)
Date: Wed Nov 22 2006 - 09:42:34 CST

Hi, all,

I tried to use nptr=1 and i found out the some 'big' problems with my
temperature, the tempi I set was 0 and the final temperature temp0 i used
was 300, however, as can be seen from the results, the tempeature jumped
suddenly from 0 to 68534 from step 0 to 1. Here are the results from the
first 5 steps.
------------------------------------------------------------------------------------

 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) = 68534.33 PRESS =
0.0
 Etot = 7845185.5440 EKtot = 8063110.8444 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 = 76.6082699232639

 NSTEP = 2 TIME(PS) = 0.000 TEMP(K) = 70569.86 PRESS =
0.0
 Etot = 8111879.0115 EKtot = 8302592.1887 EPtot = -
190713.1772
 BOND = 404.0281 ANGLE = 2152.9958 DIHED =
6632.7921
 1-4 NB = 2481.8367 1-4 EEL = 33476.3125 VDWAALS =
25973.9286
 EELEC = -261835.8824 EHBOND = 0.0000 RESTRAINT =
0.8114
 EAMBER (non-restraint) = -190713.9886
 Ewald error estimate: 0.9994E-04
 ------------------------------------------------------------------------------

 NSTEP = 3 TIME(PS) = 0.000 TEMP(K) = 8042.53 PRESS =
0.0
 Etot = 755492.6032 EKtot = 946208.8141 EPtot = -
190716.2109
 BOND = 404.0158 ANGLE = 2152.9935 DIHED =
6632.7888
 1-4 NB = 2481.8332 1-4 EEL = 33476.3270 VDWAALS =
26028.0919
 EELEC = -261893.0720 EHBOND = 0.0000 RESTRAINT =
0.8110
 EAMBER (non-restraint) = -190717.0218
 Ewald error estimate: 0.9614E-04
 ------------------------------------------------------------------------------

 NSTEP = 4 TIME(PS) = 0.000 TEMP(K) = 8041.47 PRESS =
0.0
 Etot = 755402.6856 EKtot = 946084.1780 EPtot = -
190681.4924
 BOND = 403.9985 ANGLE = 2152.9901 DIHED =
6632.7849
 1-4 NB = 2481.8324 1-4 EEL = 33476.3362 VDWAALS =
26083.5195
 EELEC = -261913.7651 EHBOND = 0.0000 RESTRAINT =
0.8110
 EAMBER (non-restraint) = -190682.3034
 Ewald error estimate: 0.8952E-04
 ------------------------------------------------------------------------------

 NSTEP = 5 TIME(PS) = 0.000 TEMP(K) = 8040.12 PRESS =
0.0
 Etot = 755316.1071 EKtot = 945925.3126 EPtot = -
190609.2055
 BOND = 403.9698 ANGLE = 2152.9937 DIHED =
6632.7807
 1-4 NB = 2481.8308 1-4 EEL = 33476.3452 VDWAALS =
26140.2300
 EELEC = -261898.1673 EHBOND = 0.0000 RESTRAINT =
0.8116
 EAMBER (non-restraint) = -190610.0171
 Ewald error estimate: 0.9264E-04
 ------------------------------------------------------------------------------

Anyone can tell me why is this happening?

Thanks a lot!

Rachel

On 11/22/06, Rachel <comeonsos_at_googlemail.com> wrote:
>
> 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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