AMBER Archive (2008)

Subject: RE: AMBER: reset time and comments

From: Ross Walker (ross_at_rosswalker.co.uk)
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 't=xxx.xxx' 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
 &cntrl
   imin =0,irest=1,ntx=5,
   nstlim=10, dt=0.0005, !sets number of steps + time step
   ntwx=0,
   nscm=0,tempi=300.0, !sets COM motion options + initial temp
   temp0=300.0,
   scee=1.2, ntpr=1,
   ntb=0, cut=999., !no periodic boundaries and large cut.
   ntt=0,
   ifqnt=1, igb=1,
 /
 &qmmm
   qmmask='@*',
   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
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | 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.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu