Hi,
Minimization does not use velocity information, only MD (which is why
you don't have velocity info in your restart to begin with), so you
don't need to set 'irest' if you are continuing a minimization.
-Dan
On Tue, May 20, 2014 at 10:14 AM, Valentina Romano
<valentina.romano.unibas.ch> wrote:
> Dear users
>
> I ran a min. step for 2500 steps.
> Since the energy was not stable and the RMS still high i decided to run a second min. (2500 additional steps) using as starting point the files i got from the previous step.
>
> In the first step:
> -r PknGAde-min.rst and -ref PknGAde-solv-min.rst
>
> The 2nd step input file was the following:
>
> Initial XMIN minimisation of PknG-Adenine complex: complex, water and ions
> &cntrl
> imin=1,
> maxcyc=2500,
> ntmin=3,
> irest=1,
> ntx=5,
> ntb=1,
> igb=0,
> ntr=0,
> cut=10,
> ntpr=10, ntwx=10, ntwr=1000
>
> And i ran sander as follow:
> sander -O -i PknGAde-min.in -o PknGAde-min.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde-min.rst -r PknGAde-min.rst -ref PknGAde-solv-min.rst -x PknGAde-min.mdcrd &
>
> Thus I used as coord. the file I got from the previuos min.
>
> I got the following error:
> ERROR: I could not find enough velocities in
> PknGAde-min.rst
>
> I do not understand why i got that error.
> Anyone can help me in understanding what happened?
>
> Thank you
> Valentina
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Tue May 20 2014 - 10:00:04 PDT
