AMBER Archive (2004)

Subject: Re: AMBER: vlimit and vmax problem

From: Rhonda Torres (torres_at_scripps.edu)
Date: Wed Mar 24 2004 - 15:05:20 CST

Hi Venkat,

Your BOND energy is quite high. I suspect there is a problem with your
structure related to this. You appear to have ntpr=50 (default). Set
ntpr=1, which will give you more information. For more assistance, we
would need to see the files.

Also, your cut value of 8.0 is a little low. The recommended cut is at
least 10.0.

Rhonda

On Wed, 24 Mar 2004, Venkata S Koppuravuri wrote:

>
> Hi Amber users,
>
> I am trying to equlibrate a protein structure and I have got the following
> error
> -----------------------
>
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
> Etot = -75506.0178 EKtot = 0.0000 EPtot = -75506.0178
> BOND = 34481.4693 ANGLE = 415.2692 DIHED = 903.4396
> 1-4 NB = 948.4239 1-4 EEL = 6679.2911 VDWAALS = 12987.2993
> EELEC = -131921.2101 EHBOND = 0.0000 RESTRAINT = 0.0000
> Ewald error estimate: 0.1421E-02
>
>
> vlimit exceeded for step 2 ; vmax = 24.48541998723091
> vlimit exceeded for step 3 ; vmax = 35.95753378509406
> vlimit exceeded for step 4 ; vmax = 77.34057453092329
> vlimit exceeded for step 5 ; vmax = 91.32961951303912
> vlimit exceeded for step 6 ; vmax = 31.87861489298826
> .....................
> .............
>
> -------------------------
>
> I have searched in google for this error and have tried all the possible
> errors mentioned .
> 1. the minimization went fine.
> 2. periodic box is correct.
> 3. checked for overlapping of molecules
> 4. i am using constant volume i.e. ntb=1
> 5. i am trying to increase temp in steps of 50k
> 6. i have increased the vlimit value (not sure whether this helps!)
>
>
> and i still get the same error. Below is the input file that i used
>
> --------------------
> &cntrl
> imin = 0, irest = 0, ntx = 1,
> nstlim = 10000, nsnb = 25,
> vlimit = 20,
> tempi = 0.0, temp0 = 50.0, ntpr = 100,
> ntt = 1, npscal = 1, ntb = 1, ntp = 0, taup = 0.2,
> ntc = 2, ntf = 2, cut = 8.0, scee = 1.2,
> ntwx= 100, ntwe = 100, ntwv = 100,
> &end
>
> END
> END
> ----------------------
>
> Can someone help me with this please
>
> Regards,
> -Venkat
>
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