AMBER Archive (2008)

Subject: Re: AMBER:

From: Boutheina Kerkeni (b.kerkeni_at_ucl.ac.uk)
Date: Fri Jul 04 2008 - 06:02:10 CDT

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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