AMBER Archive (2004)

Subject: Re: AMBER: water hole

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Apr 12 2004 - 17:40:13 CDT

why are the bond, angle, dihedral and 1-4 energies all zero?

----- Original Message -----
From: "Holly Freedman" <holly_at_mercury.hec.utah.edu>
To: <amber_at_scripps.edu>
Sent: Monday, April 12, 2004 5:43 PM
Subject: AMBER: water hole

> 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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu