Re: AMBER:

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Fri, 4 Jul 2008 07:50:44 -0400

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.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
>
>> 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.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.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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>>
>>
>>
>> --
>> ===================================================================
>> Carlos L. Simmerling, Ph.D.
>> Associate Professor Phone: (631) 632-1336
>> Center for Structural Biology Fax: (631) 632-1555
>> CMM Bldg, Room G80
>> Stony Brook University E-mail: carlos.simmerling.gmail.com
>> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
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Received on Sun Jul 06 2008 - 06:07:45 PDT
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