AMBER Archive (2004)

Subject: AMBER: water hole

From: Holly Freedman (holly_at_mercury.hec.utah.edu)
Date: Mon Apr 12 2004 - 16:43:32 CDT

We are trying to perform AMBER simulations on hydroxypyridine and
oxopyridine. We ran Gaussian using ESP to get the charge fitting and
then got an AMBER prep file and a force field modification for gaff
using antechamber. We added water, relaxed, thermalized to 298 and then
equilibrated the structure. We have been leaving the structure fixed at
the minimum energy structure from Gaussian. However about 70000 steps
into the md, we started to get messages about vlimit being exceeded and
also vmax = nan. Would you please have a look at my input and the
output meesage and give me your advice on how to fix the input?
Here's the input file for the md run:

&cntrl
  imin = 0,
  ntx = 1, irest = 0, ibelly = 1,
  ntpr = 100, ntwr = 100, iwrap = 1,
  ntwx = 100, ntwe = 5000,
  ntf = 2, ntb = 2, cut = 10,
  nstlim = 100000, dt = .002,
  tempi = 298, temp0 = 298, ntt = 1,
  ntp = 1, taup = 1.0,
  ntc = 2,
 &end
Moving region
 RES 2 826
END
END

Here is the error message in the output file:

 NSTEP = 74200 TIME(PS) = 159.400 TEMP(K) = 420.11 PRESS = -154.6
 Etot = -5216.0784 EKtot = 2066.2222 EPtot = -7282.3006
 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1031.1950
 EELEC = -8313.4956 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 1040.4340 VIRIAL = 1136.4725 VOLUME = 28777.8501
                                                Density = 0.8631
 Ewald error estimate: 0.1118E-01
 ------------------------------------------------------------------------------

 vlimit exceeded for step 74238; vmax = nan
 vlimit exceeded for step 74239; vmax = nan
 vlimit exceeded for step 74240; vmax = nan
 vlimit exceeded for step 74241; vmax = nan

We did some analysis on the coordinate files that were obtained after
thermalizing and equilibrating my pyridine molecules. Everything looked
fine until after the equilibriration; then a hole seems to be formed in
the water box close to the solute molecule. Have you ever had any
experiences with the formation of such channels in the past? Here is the
equilib.in file:

&cntrl
 imin = 0,
 ntx = 1, irest = 0, ibelly = 1,
 ntpr = 100, ntwr = 100, ntwx = 100, ntwe = 100,
 ntf = 2, ntb = 2, cut = 10,
 nstlim = 10000, dt = .001, ntc = 2,
 tempi = 298.0, temp0 = 298.0, ntt = 1,
 tautp = 1.0, ntp = 1,
&end
Moving region
RES 2 826
END
END

Also do you think that a newer version of antechamber might help? We
are using the version that comes with amber 7.
I would appreciate any suggestions that you can make. Thanks,
-- Holly Freedman
Dept. of Chemistry
University of Utah

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