AMBER Archive (2005)

Subject: RE: AMBER: Tutorial question and some more...

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Aug 09 2005 - 14:03:01 CDT

Dear Pawel,

> Is it a good way to minimise a structure e.g. peptide at first in
> the vacuum then add water and do steps a) minimise with ntr=1 then
> b) minimise whole structure?

This depends on how good your initial structure is. If your initial
structure was built by hand then you may need to be careful when minimising
or running MD and doing things in stages can help. Often though this isn;t
necessary and you can just do a few hundred steps of minimisation on the
whole system without restraints. The reason it is done in two stages in the
tutorials is more as a way of introducing how to use restraints than is
actually needed to initially minimise the structure.

> My second question is about Beginners Tutorial part 5 (Running
> minimisation in explicit water). Why in the minimisation stage the
> constant pressure is not on? Is it because of low temperature?

By this I guess you mean tutorial 1 part 5 and are refering to the two
minimisation stages and the initial heating stage. Here constant volume is
used and then when we change to equilibration constant pressure is used. You
are correct in your assumption, when you are at very low temperatures the
calculation of pressure is very inaccurate so you can get these huge swings
which cause the barostat to overcompensate resulting in an unstable
trajectory. It is much more stable to do the minimisation and heating at
constant volume and then switch to constant pressure. Although you don't
always need to do this, it is generally just good practice...

> My third question is about something else :-)
> What I can do (besides looking) when in my output minimisation
> sander "battles" with one atom, and in the end it is written
> "RESTARTED DUE TO LINMIN FAILURE"(all knows what it means), and I
> would really like to do minimisation stage till the end.

Do you have shake on? If you have shake on you won't be able to minimise to
a very low RMS because the sander minimiser is not designed to really handle
shake properly. Secondly the minimiser in sander is not really designed to
get you all the way down to a local minima so for big systems will often
fail while the RMS is still quite high. If you really really want to get
close to a local minima then you really need a minimiser that uses second
derivatives such as Newton Raphson. I think you can probably use nmode to do
this as it contains a NR minimiser. Although for systems of more than a few
thousand atoms you will have problems as storing second derivatives needs
lots of memory.
 
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_at_rosswalker.co.uk |
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