AMBER Archive (2004)

Subject: Re: AMBER: Problem with Water solute during MD

From: Daniel Wetzler (danielwetzler_at_appleinfo.de)
Date: Wed Nov 10 2004 - 04:19:11 CST

Hi David and all,

I repeated my experiemenrtt several times and got the folowing eresults.
My program version is AMBER 7, running on LINUX.
My configuration file looks like that :

 molecular dynamics
 &cntrl
  irest = 0, ntx = 1,
  ntb = 2, ntp = 2,
  nstlim = 1000,
  dt = 0.001,
  ntpr = 500,
  ntwx = 500,
  ntwv = 500,
  ibelly = 1,
  ntt=1, temp0 = 300., tempi = 0.,
  cut = 8.0,
  scee = 1.2,
  ntf = 2,
  iwrap = 1,
  ntc = 2,
 &end
WATER
RES 284 4784
END
END
eof

This is the file which would work (all waters fixed).

If I turn ibelly off I get something like that :

 ---------------------------------------------------
 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 = 0.3242E-14 at 2.436720
| CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 2163276
| TOTAL SIZE OF NONBOND LIST = 2163276

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =********
 Etot = ************ EKtot = 0.0000 EPtot = ************
 BOND = 114.2394 ANGLE = 511.8678 DIHED = 1184.2036
 1-4 NB = 823.3046 1-4 EEL = 12974.1609 VDWAALS = ************
 EELEC = -45507.8938 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 0.0000 VIRIAL = ************ VOLUME = 191472.4309
                                                Density = 0.7724
 Ewald error estimate: 0.6883E-04
 ------------------------------------------------------------------------------

 vlimit exceeded for step 0; vmax = 128032.551
 EWALD BOMB in subroutine ewald_list
  volume of ucell too big, too many subcells
  list grid memory needs to be reallocated, restart sander

So it seems that AMBER 7 can't handle so many water molecules.
But during the equilibration it did handle all the water.
Do I have to change some value within the header files and recompile ?
Or is there a massive error within my config file ?

Best wishes,

Daniel

David A. Case wrote:

>On Tue, Nov 09, 2004, Daniel Wetzler wrote:
>
>
>>I'm trying to perform a MD run on a molecule soluted
>>in Water (WATBOX216).
>>The molecule was equilibrated with a EM.
>>Interestingly the resulting restart-file didn't have any box
>>information anymore (I had to copy the box manually
>>into the restart file).
>>
>>
>
>We need more details about your input file. It sounds like maybe you did
>not set ntb>0 (?). Also, be sure to indicate which version of Amber you
>are running.
>
>
>
>>My problem is, that the MD crashes without Error
>>but with a coredump.
>>
>>
>
>See above: we can't possibly help without more information.
>
>....dac
>
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