RE: AMBER: the problem of mdcrd

From: Ross Walker <ross.rosswalker.co.uk>
Date: Mon, 16 Jan 2006 08:44:11 -0800

Dear Xiphias,

The ****'s are written to the mdcrd file when the value becomes too big for
the space allocated for it in the code. In this case -999.999 < x > 9999.999
A

Thus, unless your system is very big one of two things is likely causing the
problem.

1) You initial coordinates are a long way from the the origin. Create a pdb
file from the inpcrd file and see what you get for the typical coordinate
range. If your initial system is a close to exceeding the limit then try
using ptraj to recenter this coordinates and create a new inpcrd file.

2) Your system is blowing up. Check the output file, are your temperatures
abnormally high? Say >500K ? if so then your system has likely expanded very
rapidly and thus one or more atoms has moved a long way from the initial
structure. What do the first 47 frames of the trajectory look like? Do they
make sense? What happens if you setup your system to run 47*250 steps and
then run another 500 steps as a restart but with ntwx=1. Then you can watch
a very fine grain version of the trajectory and see if anything is going
astray.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of xiphias xie
> Sent: Monday, January 16, 2006 01:16
> To: amber.scripps.edu
> Subject: AMBER: the problem of mdcrd
>
> Dear Amberers:
>
> I encountered a strange problem in running MD
> Equilibration on the whole system . My job is normaly
> ended ,the .out file is complete.but when i see the
> .mdcrd file by using VMD ,it just display a part of
> the trajectiory. when i run ptraj to calculate the
> RMSD,it displays that:
>
> ERROR in readAmberTrajectory(): Set #48 has coordinate
> out of bounds (i.e. *****'s)
> PTRAJ: Successfully read in 47 sets and processed 47
> sets.
> the total sets is not 47 sets ,but 1000 sets .
> here is my .in file:
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 356.65, temp0 = 300.0,
> ntt = 1,
> nstlim = 250000, dt = 0.002,
> ntpr = 250, ntwx = 250, ntwr = 1000
> /
> I repeated it 3 times ,i encountered this every time
> .
> Could you please give me a suggestion?
>
> Thank you very much in advance !
> xiphias
>
>
>
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