AMBER Archive (2004)

Subject: RE: AMBER: MD problem (very long parhabs endless runtime)

From: Ross Walker (
Date: Sat Oct 23 2004 - 11:57:39 CDT

Dear Daniel,

> now without any results. There's no error and the program
> takes the full
> load of the computer (PIV 2.6 GHz). I assumed that a single

Do you get any output at all? E.g. if you look in the mdout file has the
input file at least been reported here?

Also, how big is your system? A single step for anything up to 100,000 atoms
really should not take more than a minute at most.

Are you running this on a single cpu? Or in parallel on the machine?
(mpirun). Also do the test cases all pass? It likely that if you are getting
no output at all that you sander installation is corrupt. If the test cases
all pass then this is much more unlikely.

> molecular dynamics
> &cntrl
> irest = 0, ntx = 1,

This bit looks fine.

> ntb = 2, ntp = 0,

This part of your input is inconsistent. You are requesting a constant
pressure run (ntb=2) but then set there to be "NO" pressure scaling (ntp=0).
This is likely to be the cause of your problem if all the test cases pass.
However, sander should really have produced an error message in this

> nstlim = 10,

If you really only want one step you should set this to nstlim=1. Note btw,
if you are interested in just obtaining the energy for the "current"
structure then you are better off doing a single step of minimisation rather
than MD. (set imin=1 and maxcyc=1). In this way the energy of the initial
structure will be calculated but no actual structural changes will take

> dt = 0.001,
> ntpr = 1,
> ntwx = 1,

This is fine.

> ntwv = 1,

Do you 'really' want to write out the velocities every step? If at all?

> ibelly = 1,

Belly should work but is not recommended practice any more. Especially if
you are trying to do constant pressure MD. This is unlikely to give you a
stable simulation. I would avoid belly for anything other than
minimisation...!!! And even then you are probably better using restraints

> ntt=1, temp0 = 300., tempi = 300.,
> cut = 9.0,
> scee = 1.2,
> ntf = 2,

This is fine - assuming your system is stable enough to simply start it out
at 300K.

> iwrap = 1,

Iwrap is fine but not really necessary. You are much better off just post
processing the trajectory with ptraj and using this to wrap the system back
into the central box.

> ntc = 2,
> &end
> RES 278 278
> RES 279 279
> RES 281 2470


What is this QUIT line? It isn't needed.

I hope this all helps...
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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