something doesn't seem right, your density is not going down like it should.
can you email the entire output file directly to me? maybe I'll see
something.
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
Agata Jurkiewicz wrote:
>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.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.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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>>>
>>>
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Received on Fri Jul 22 2005 - 20:53:01 PDT
