AMBER Archive (2008)

Subject: Re: AMBER:

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jul 04 2008 - 07:37:29 CDT

0 energy only makes sense if you changed the reference structure for every run.
I don't usually do that as it makes the restraint forces and energy
discontinuous
for each restart. I keep the same reference structure until restraints
are turned off,
or else you get discontinuity and structure drift.

On Fri, Jul 4, 2008 at 8:27 AM, Boutheina Kerkeni <b.kerkeni_at_ucl.ac.uk> wrote:
> It is always the case in md.out the first results for NSTEPS=0 gives
> RESTRAINT = 0.0000.
> whether you specify restraints or not.
>
> The pb is with the message amber gives me in the log:
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 4583 9292 9293
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
>
>> I'm still confused about the restrains- you define them in the
>> md input but there is no restraint energy- why?
>>
>> On Fri, Jul 4, 2008 at 7:44 AM, Boutheina Kerkeni <b.kerkeni_at_ucl.ac.uk>
>> wrote:
>>>
>>>
>>>> the bond energy here is really high. have you looked at the structure
>>>> to see why? look at atom 5941, which has the Gmax
>>> The distance between the orginal 5914 and final 6914 atom is 1.5 Å
>>>
>>>> it's hard to diagnose because the restraints might be holding it
>>>> in a high energy structure. It is also difficult because you are mixing
>>>> belly and restraints, so hard to visually check things.
>>>> have you tried using only restraints, or is there some reason that
>>>> part of the structure must be absolutely constrained?
>>>>
>>> yes, its geometry needs to be fixed. I trained the constraint approach
>>> for
>>> it but it resulted in unphysical distorsion of part2.
>>>> actually now that I look closer I am confused- why is the
>>>> restraint energy zero if you are using restraints? are you sure they
>>>> were
>>>> read properly? look in the sander output.
>>>>
>>> Yes, what I copied was part of minimisation, so no restraints at all,
>>> first one being restraints on protein only.
>>>
>>> The md pb may be comes from the ibelly group, is it usual to run
>>> successful md with ibelly?
>>> Thanks
>>> B
>>>> On Fri, Jul 4, 2008 at 7:02 AM, Boutheina Kerkeni <b.kerkeni_at_ucl.ac.uk>
>>>> wrote:
>>>>> Thanks you so much for the suggestions.
>>>>> This is the last part of my minimization output from which my md
>>>>> started
>>>>>
>>>>> NSTEP ENERGY RMS GMAX NAME
>>>>> NUMBER
>>>>> 2500 -8.1802E+03 2.8384E-01 4.8230E+01 NH1
>>>>> 5914
>>>>>
>>>>> BOND = 42002.5713 ANGLE = 2640.3485 DIHED =
>>>>> 6628.7767
>>>>> VDWAALS = 284231.0709 EEL = -380927.6059 HBOND =
>>>>> 0.0000
>>>>> 1-4 VDW = 2527.0010 1-4 EEL = 34717.6394 RESTRAINT =
>>>>> 0.0000
>>>>>
>>>>>
>>>>> Maximum number of minimization cycles reached.
>>>>>
>>>>>
>>>>> FINAL RESULTS
>>>>>
>>>>>
>>>>>
>>>>> NSTEP ENERGY RMS GMAX NAME
>>>>> NUMBER
>>>>> 2500 -8.1802E+03 2.8384E-01 4.8230E+01 NH1
>>>>> 5914
>>>>>
>>>>> BOND = 42002.5713 ANGLE = 2640.3485 DIHED =
>>>>> 6628.7767
>>>>> VDWAALS = 284231.0709 EEL = -380927.6059 HBOND =
>>>>> 0.0000
>>>>> 1-4 VDW = 2527.0010 1-4 EEL = 34717.6394 RESTRAINT =
>>>>> 0.0000
>>>>> I checked with VMD the minimized pdb file and it lookes fine, part1
>>>>> moved
>>>>> a little but part 2 frozen. Is there another check to make sure every
>>>>> thing went fine?
>>>>> - Also As you suggested I started from tempi=300 tempf=300
>>>>> but still got the same error message
>>>>> vlimit exceeded for step 1; vmax = 210.0493
>>>>>
>>>>>> it might be because you are heating from 0K to 300K very quickly.
>>>>>> you might try slower heating, or assign tempi of at least 200K, maybe
>>>>>> even 300K (it depends on your system and how careful you need to
>>>>>> be with equilibration, but it's something to at least try in order to
>>>>>> identify
>>>>>> the problem).
>>>>>>
>>>>>> the initial bond and vdw energies are really high - are you sure the
>>>>>> minimization went as well as you think? is the initial energy here
>>>>>> the
>>>>>> same
>>>>>> as the final energy from minimization? the vdw seems too high, even
>>>>>> with
>>>>>> explicit water (which usually has large vdw but even larger negative
>>>>>> electrostatic)
>>>>>> carlos
>>>>>>
>>>>>> On Fri, Jul 4, 2008 at 6:34 AM, Boutheina Kerkeni
>>>>>> <b.kerkeni_at_ucl.ac.uk>
>>>>>> wrote:
>>>>>>> Hi AMber Users
>>>>>>>
>>>>>>> I am running an first stage md on my system composed of a
>>>>>>> [protein(part1)
>>>>>>> + (part2) ] solvated and neutralized.
>>>>>>>
>>>>>>> I want part2 to be frozen, so I did using belly. Minimizations went
>>>>>>> fine.
>>>>>>> When I start the md job:
>>>>>>>
>>>>>>> &cntrl
>>>>>>> imin = 0,
>>>>>>> irest = 0,
>>>>>>> ntx = 1,
>>>>>>> ntb = 1,
>>>>>>> cut = 10,
>>>>>>> ntr = 1,
>>>>>>> ntc = 2, ntf = 2,
>>>>>>> tempi = 0.0,
>>>>>>> temp0 = 300.0,
>>>>>>> ntt = 3,
>>>>>>> gamma_ln = 1.0,
>>>>>>> nstlim = 10000, dt = 0.002,
>>>>>>> ntpr = 100, ntwx = 100, ntwr = 1000,
>>>>>>> ibelly=1
>>>>>>> /
>>>>>>> Keep protein fixed with weak restraints
>>>>>>> 10.0
>>>>>>> RES 1 796
>>>>>>> END
>>>>>>> END
>>>>>>> Keep part2 fixed with belly
>>>>>>> ATOM 1 12180 20821 80124
>>>>>>> END
>>>>>>> END
>>>>>>>
>>>>>>>
>>>>>>> The calculation stops with an error :
>>>>>>> --------------------------------------------------------------------------------
>>>>>>> 4. RESULTS
>>>>>>> --------------------------------------------------------------------------------
>>>>>>>
>>>>>>> ---------------------------------------------------
>>>>>>> APPROXIMATING switch and d/dx switch using CUBIC SPLINE
>>>>>>> INTERPOLATION
>>>>>>> using 5000.0 points per unit in tabled values
>>>>>>> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>>>>>>> | CHECK switch(x): max rel err = 0.3338E-14 at 2.509300
>>>>>>> | CHECK d/dx switch(x): max rel err = 0.8155E-11 at 2.730040
>>>>>>> ---------------------------------------------------
>>>>>>> | Local SIZE OF NONBOND LIST = 1429347
>>>>>>> | TOTAL SIZE OF NONBOND LIST = 24009616
>>>>>>>
>>>>>>> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00
>>>>>>> PRESS
>>>>>>> =
>>>>>>> 0.0
>>>>>>> Etot = -30003.2906 EKtot = 0.0000 EPtot =
>>>>>>> -30003.2906
>>>>>>> BOND = 20179.4792 ANGLE = 2640.3486 DIHED =
>>>>>>> 6628.7767
>>>>>>> 1-4 NB = 2527.0010 1-4 EEL = 34717.6394 VDWAALS =
>>>>>>> 284231.0709
>>>>>>> EELEC = -380927.6064 EHBOND = 0.0000 RESTRAINT =
>>>>>>> 0.0000
>>>>>>> Ewald error estimate: 0.2038E-04
>>>>>>> ------------------------------------------------------------------------------
>>>>>>>
>>>>>>> vlimit exceeded for step 1; vmax = 214.0560
>>>>>>>
>>>>>>>
>>>>>>> Also in the log file the following message appears
>>>>>>> -------------------------------------------
>>>>>>> Job started at Fri Jul 4 11:25:26 BST 2008
>>>>>>> -------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>> Coordinate resetting (SHAKE) cannot be accomplished,
>>>>>>> deviation is too large
>>>>>>> NITER, NIT, LL, I and J are : 0 0 4824 9785 9787
>>>>>>>
>>>>>>> Note: This is usually a symptom of some deeper
>>>>>>> problem with the energetics of the system.
>>>>>>>
>>>>>>> --------------------------------------------
>>>>>>> Job finished at Fri Jul 4 11:25:46 BST 2008
>>>>>>>
>>>>>>>
>>>>>>> Any idea if someone has already seen such a pb?
>>>>>>> Thanks very much for your help!
>>>>>>> Regards
>>>>>>> Boutheina
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>
>>>>>
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>>>>
>>>>
>>>>
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