AMBER Archive (2003)

Subject: Re: AMBER: Reverse TI run

From: Martin Lepsik (lepsik_at_marilyn.uochb.cas.cz)
Date: Tue Oct 14 2003 - 08:02:22 CDT

Dear Mike,
I have mended the rst file as you proposed and submitted the jobs into the
queue. I hope it'll turn out well.

Thanks for your advice,

Martin

P.S. What's the future of FEP/TI calculations in AMBER? Is gibbs going to be
replaced by SANDER or yet by another program?

> Dear Martin,
> You are right about the restart file from gibbs.
> There is very little (read that no) development in gibbs anymore
> and nobody is checking to make sure that it is keeping up with
> sander development.
>
> The philosophy has changed to be that the box information is
> state information and belongs in the restart/coordinate file.
> If you are running constant volume (I did not take the time to
> look at your input) you can use the information in the prmtop
> file, fix the format, and put it at the end of the restart file
> from gibbs. That ought to do the trick.
>
> There should be a part of the prmtop that looks like:
>
> %FLAG BOX_DIMENSIONS
> %FORMAT(5E16.8)
> 9.00000000E+01 2.79683980E+01 2.97180970E+01 2.61915520E+01
>
> The first number is the angle, the other three are the box dims.
> Try putting a like like:
> 27.9600000 29.7200000 26.1900000 90.0000000 90.0000000 90.0000000
>
> at the end of the restart file.
> That is all assuming that your box is rectangular, if it is truncated
> octahedron or some other shape, your angles will need to be different.
> If you ran at all with constant pressure, you will need to find the
> latest box sizes to use at the end of the restart file.
>
> Mike
>
>

Dear AMBER community,
I run thermodynamic integration in a box of water in a batch series: sander
equilibrate, gibbs perturb, sander equilibrate, gibbs perturb in reverse
direction. The error message is

 getting new box info from bottom of inpcrd

It is true I cannot see any box info in the Pert.rst file.

Should I set this? How shall irest and ntx be specified in "reverse" sander
run?

Thanks for your advice.

Best regards,

Martin Lepsik
>
>

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