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.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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Received on Fri Jul 22 2005 - 18:53:00 PDT
