hello,
Once time, I had the same problem:
> COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
> DEVIATION IS TOO LARGE
> NITER, NIT, LL, I AND J ARE : 0 0 42 83 84
>
To solve it, I increased the size of the water box. Maybe, this can solve your
problem.
PB
> I have been working with "cubes" of water, but I wanted to try a TO. I
> have a small 20 residue peptide structure that I've placed in a TO using
> the procedure in the Amber6 tutorial (leap gives a cube using WATBOX216,
> ptraj chops it into a TO using "truncoct :1-20 10.0 prmtop oct_top.prm")
>
> I then minimized the water while fixing residues 1-20 and then minimized
> the entire system. I then started a 10ps MD run in which residues 1-20
> were again fixed. Looking at the resulting structure (I used iwrap=1), I
> noticed my peptide is very close to one edge of the TO, leading to my
> first question:
>
> 1) Does it matter if my solute of interest appears to get near an edge of
> the TO using iwrap=1, or does this make no difference from a simulation
> point of view.
>
> My bigger problem is that if I take the coordinate file (restrt) from that
> run and then try to apply it to a long runner with no fixed residues,
> sander immediately crashes with:
>
> NSTEP = 0 TIME(PS) = 100.000 TEMP(K) = 727.10 PRESS =**********
> Etot = ************ EKtot = 9000.9543 EPtot = ************
> BOND = 104.0038 ANGLE = 242.8940 DIHED = 144.2317
> 1-4 NB = 76.9501 1-4 EEL = 871.9589 VDWAALS = ************
> EELEC = -11424.0419 EHBOND = 0.0000 CONSTRAINT = 0.0000
> EKCMT = 2817.9106 VIRIAL = ************ VOLUME = 85720.1675
> Density = 0.7229
> Ewald error estimate: 0.1067E-03
>
> ------------------------------------------------------------------------------
>
>
> COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
> DEVIATION IS TOO LARGE
> NITER, NIT, LL, I AND J ARE : 0 0 42 83 84
>
> This doesn't make sense to me, as the final mdinfo written in the first md
> run ans the starred values within ok ranges:
>
> NSTEP = 10000 TIME(PS) = 10.000 TEMP(K) = 493.15 PRESS = -237.87
> Etot = -7754.5543 EKtot = 6104.7889 EPtot = -13859.3431
> BOND = 97.1805 ANGLE = 228.5314 DIHED = 149.7346
> 1-4 NB = 73.3083 1-4 EEL = 855.4814 VDWAALS = 1369.0613
> EELEC = -16632.6405 EHBOND = 0.0000 CONSTRAINT = 0.0000
> EKCMT = 2827.3824 VIRIAL = 3275.7318 VOLUME = 87296.2099
> Density = 0.7099
> Ewald error estimate: 0.3716E-03
>
> So question two:
>
> 2) Why can't I get an MD run to start in Sander using the restrt file from
> my previous run? (I've never had this type of problem with cubes)
>
> Thanks for your help. I've included my second MD run file below.
>
> Robert
>
> &cntrl
> imin=0,
> irest=0,
> ntpr=100,
> ntwr=100,
> ntwx=1000,
> ntwe=100,
> ntf=2,
> ntb=2,
> nstlim=50000,
> dt=.001,
> temp0=498,
> tempi=498,
> ntt=1,
> tautp=1.0,
> ntp=1,
> taup=1.0,
> ntc=2,
> iwrap=1,
> &end
>
>
> _________________________
> R. M. Fesinmeyer
> rmf_at_u.washington.edu
> Department of Chemistry
> University of Washington
>
>-- End of excerpt from Robert Matthew Fesinmeyer
--
********************************************************************************
Pascal Bonnet pascal_at_qorws1.uab.es
Unitat Quimica Organica and Institut de Chimie Organique et Analytique
Facultat de Ciences UFR Sciences - UMR 6005
Universitat Autonoma de Barcelona Rue de Chartres - BP 6759
08193 Bellaterra (SPAIN) 45067 ORLEANS CEDEX 2 - France
Tel: 34935811266 Tel: 0238494577
Fax: 34935811265
********************************************************************************
Received on Fri Nov 17 2000 - 10:12:30 PST
