AMBER Archive (2008)

Subject: RE: AMBER: reset time and comments

From: Ross Walker (
Date: Thu May 08 2008 - 10:24:50 CDT

> The first one is: Is it possible to reset the "time" in an MD simulation?.
> ( I am restarting the simulation and would like my times in the output
> file to start at 0)

You can set the time manually with '' in the &cntrl namelist,
however this will be ignored if irest=1, I.e. you are restarting a
simulation and reusing the velocities. You can work around this by editing
the first line of the restart file where you will see the time printed -
changing this will change the time printed in the mdout file.
> Question 2:
> Is it possible to write comments on input files?.
> this way I dont forget what my scripts do :)

You can use an '!' at the end of lines in order to include comments. I.e.

NMA: 10 steps MD - Pure QM/MD - no temperature coupling
   imin =0,irest=1,ntx=5,
   nstlim=10, dt=0.0005, !sets number of steps + time step
   nscm=0,tempi=300.0, !sets COM motion options + initial temp
   scee=1.2, ntpr=1,
   ntb=0, cut=999., !no periodic boundaries and large cut.
   ifqnt=1, igb=1,
   qm_theory='PM3', qmcharge=0, qmgb=0

However, this may be implementation specific - also the maximum line length
may also be implementation specific so your mileage may vary - I would just
try it and see how you get on.

All the best

|\oss Walker

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

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