AMBER Archive (2005)

Subject: Re: AMBER: SHAKE error

From: Agata Jurkiewicz (aggresja_at_gmail.com)
Date: Fri Jul 22 2005 - 12:01:16 CDT

Dear all,

Thank you for the hints.
I've changed tautp to 0.1 and dt to 0.01, like in the following
md.in file:

Amber 8, eqlbrtn, tighter T coupling, shorter timestep
  &cntrl
   imin=0, irest=1, ntx=7, ntp=1, nstlim= 25000,
    ntb=2, dt=0.001, ntt=1, temp0=300, tempi=300,
    ntpr=50, ntwr=500, scee=1.2, ntf=2, ntc=2,
    cut=12, ntwe=500, ntwx=500, ntave=5000, tautp=0.1,
  /

and I got the same error:

 ------------------------------------------------------------------------------

 NSTEP = 11150 TIME(PS) = 61.150 TEMP(K) = 306.32 PRESS = -230.4
 Etot = -5640.8341 EKtot = 1331.5608 EPtot = -6972.3949
 BOND = 4.0540 ANGLE = 16.6087 DIHED = 18.7644
 1-4 NB = 7.6254 1-4 EEL = -110.2309 VDWAALS = 1003.5220
 EELEC = -7912.7383 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 678.7378 VIRIAL = 813.9172 VOLUME = 27177.9465
                                                    Density = 0.8069
 Ewald error estimate: 0.2231E-03
 ------------------------------------------------------------------------------

 NSTEP = 11200 TIME(PS) = 61.200 TEMP(K) = 350.78 PRESS = 89.5
 Etot = -5152.2922 EKtot = 1524.8442 EPtot = -6677.1364
 BOND = 4.7864 ANGLE = 18.1522 DIHED = 17.5435
 1-4 NB = 7.3642 1-4 EEL = -109.3920 VDWAALS = 986.6305
 EELEC = -7602.2212 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 718.5220 VIRIAL = 666.0079 VOLUME = 27162.1711
                                                    Density = 0.8073
 Ewald error estimate: 0.6946E-02
 ------------------------------------------------------------------------------

 vlimit exceeded for step 11219 ; vmax = 90.6208338121492
 vlimit exceeded for step 11220 ; vmax = 24.0436241869450
 vlimit exceeded for step 11221 ; vmax = 21.0147137180043
 vlimit exceeded for step 11222 ; vmax = 29.6531277833188
 vlimit exceeded for step 11223 ; vmax = 29.2131390335408
 vlimit exceeded for step 11224 ; vmax = 22.7352810858752
 vlimit exceeded for step 11225 ; vmax = 20.9179801379055
 vlimit exceeded for step 11226 ; vmax = 21.0721474627654
 vlimit exceeded for step 11227 ; vmax = 24.1169069755573
 vlimit exceeded for step 11228 ; vmax = 20.2218187250374
 vlimit exceeded for step 11229 ; vmax = 22.7729449218372
 vlimit exceeded for step 11230 ; vmax = 23.5282680992668
 vlimit exceeded for step 11231 ; vmax = 22.9911654604639
 vlimit exceeded for step 11232 ; vmax = 21.8717438846248
 vlimit exceeded for step 11233 ; vmax = 21.1813303711289
 vlimit exceeded for step 11234 ; vmax = 20.2556438438652
 vlimit exceeded for step 11235 ; vmax = 31.9915759201488
 vlimit exceeded for step 11236 ; vmax = 20.7665550287679
 vlimit exceeded for step 11237 ; vmax = 21.2590661709873
 vlimit exceeded for step 11238 ; vmax = 20.7282912115994
 vlimit exceeded for step 11239 ; vmax = 20.4658103371141
 vlimit exceeded for step 11240 ; vmax = 20.5862925288465
 vlimit exceeded for step 11241 ; vmax = 20.3136359100207
 vlimit exceeded for step 11242 ; vmax = 20.1297329076364
 vlimit exceeded for step 11243 ; vmax = 22.3971345304708

     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.

During the first 10 ps of this equilibrations, the temperature never
exceeds 310 K. It is after 10 ps when it starts to blow up.
I will try to heat the system slower, to remove the CM motions and so
on, but I am slowly running out of ideas...

Best regards,
Agata.

On 7/22/05, David A. Case <case_at_scripps.edu> wrote:

>
> Let me add to what Carlos said: you have a big step size (0.002) and still
> a low density (0.8) but a high temperature (480K). This can readily lead
> to SHAKE failures.
>
> A good prescription is to heat to a stable 300K at constant volume, then
> switch to constant pressure, not allowing the temperature to rise very much
> when you do that. It is not all that uncommon for equilibrations to require
> shorter time steps (like .001), and smaller values for tautp.
>
> ...good luck....dac
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