AMBER Archive (2009)

Subject: RE: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input

From: Ross Walker (
Date: Tue Aug 25 2009 - 12:55:39 CDT

Hi Ashish,

> With these many atoms i feel implicit solvent is better if i am keeping
> high
> cut values for the explicit solvent minimization. Just correct about
> me.

It is NOT simply a question of the number of atoms as to whether implicit or
explicit solvent should be used. This is very much a question of what you
want to learn from a simulation and what your goals are. Note with >4000
atoms using no cut off implicit solvent could very well be slower than the
equivalent system explicitly solvated.

My opinion with regards to the use of electrostatic cutoffs in GB is that
they should not be used, you should set cut to a much larger value than the
size of your system. Others may differ in this opinion and indeed an
extensive test of the effect of a cut off in this situation should probably
be tested.

> Also let me know how to get the source code of AMBER for implementing
> some
> customized changes.

The source code comes with your AMBER installation. See $AMBERHOME/src/

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

AMBER mailing list