Hi, Ben, Andy,
Tell me exactly what you want. You would write out coords from the
xmin wrapper, but the exact place may depend on what your goal is.
Best,
Istvan
Quoting Andreas Goetz <agoetz.sdsc.edu>:
> Hi Ben,
>
> Ben Roberts wrote:
>> Hi all,
>>
>> I'm wondering if someone could give me a few pointers here.
>>
>> I'm trying to include writing restart and trajectory files in the
>> XMIN algorithm, initially for my use in QM/MM calculations, so I
>> can save files at each step instead of having to go back to the
>> start if the calculation fails (since each step may take an hour or
>> more).
>>
>> My initial solution, which works passably well, was to call minrit
>> and corpac (based on ntwr and ntwx) at the end of the main do loop
>> in run_xmin. (At the moment, this is only done if run_xmin is
>> called directly, not from run_lmod.) This is based on
>> n_force_calls. The problem is that some steps do more than one
>> force call, so that a trajectory written on every force call
>> contains more steps than the corresponding mdout file. Ideally, the
>> steps counted to determine ixdump and itdump would be those that
>> are counted for mdout-writing purposes.
>
> Each xmin step does a line search which requires several gradient
> evaluations (force calls). You don't want to write coordinates during
> the line search but only for each new xmin step.
>
>> Inside the do loop, I can see a rather complicated case switch, and
>> it's not obvious to me which branches start a new "step", and which
>> ones do another force evaluation within the same "step". Could
>> anyone clarify which is which? I would guess that "case
>> (CALCENRG_NEWNBL, CALCGRAD_NEWNBL, CALCBOTH_NEWNBL)" does not do a
>> new step and that "case (CALCENRG_OLDNBL, CALCGRAD_OLDNBL,
>> CALCBOTH_OLDNBL)" does, but I'm not certain...
>
> As far as I can see, a new xmin step is done for
>
> case ( CALCENRG_NEWNBL, CALCGRAD_NEWNBL, CALCBOTH_NEWNBL )
>
> which is also when the minimization progress is printed. This is where
> you want to write the coordinates.
>
> All the best,
> Andy
>
>> Thanks!
>>
>> Ben
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
> --
> Dr. Andreas W. Goetz
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Sat May 08 2010 - 01:30:03 PDT
