AMBER Archive (2005)

Subject: Re: AMBER: SHAKE error

From: Agata Jurkiewicz (aggresja_at_gmail.com)
Date: Fri Jul 22 2005 - 14:12:10 CDT

Dear Carlos,
I set the taup and nscm values as you said.
The md.in file was:

Amber 8, eqlbrtn, tautp, dt, taup, nscm
  &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,
    taup=0.1, nscm=500,
  /

and I got:

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

 NSTEP = 3650 TIME(PS) = 53.650 TEMP(K) = 299.00 PRESS = -255.0
 Etot = -5561.8621 EKtot = 1299.7657 EPtot = -6861.6278
 BOND = 2.6922 ANGLE = 14.2009 DIHED = 18.4842
 1-4 NB = 7.4124 1-4 EEL = -110.8240 VDWAALS = 986.7654
 EELEC = -7780.3589 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 641.4689 VIRIAL = 792.3375 VOLUME = 27397.4782
                                                    Density = 0.8004
 Ewald error estimate: 0.9212E-03
 ------------------------------------------------------------------------------

 NSTEP = 3700 TIME(PS) = 53.700 TEMP(K) = 307.40 PRESS = -450.0
 Etot = -5262.1523 EKtot = 1336.2483 EPtot = -6598.4006
 BOND = 2.1473 ANGLE = 13.0797 DIHED = 18.5123
 1-4 NB = 7.3526 1-4 EEL = -107.8698 VDWAALS = 895.6960
 EELEC = -7427.3188 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 658.1033 VIRIAL = 921.7630 VOLUME = 27133.5024
                                                    Density = 0.8082
 Ewald error estimate: 0.6514E-02
 ------------------------------------------------------------------------------

 vlimit exceeded for step 3747 ; vmax = 3278.16945276281
 SANDER BOMB in subroutine nonbond_list
  volume of ucell too big, too many subcells
  list grid memory needs to be reallocated, restart sander

What does it mean? Should I just restart the simulation and not worry?

Regards,
Agata.

On 7/22/05, Carlos Simmerling <carlos.simmerling_at_stonybrook.edu> wrote:
> 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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