AMBER Archive (2005)

Subject: Re: AMBER: SHAKE error

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Fri Jul 22 2005 - 12:24:46 CDT

I still think you should try smaller taup and setting mscm as well.
your density is low and EKCMT is high.
also like Dave Case said, you may not have run the
previous steps long enough to get a _stable_ constant V
system.

Agata Jurkiewicz wrote:

>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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