it can often be useful to extract the rms value along the minimization and
plot it, seeing if it is still going down.
On Thu, Feb 12, 2009 at 9:11 AM, Daniel Emery <Daniel.Emery.unige.ch> wrote:
> I actually have run this optimization for 150'000 steps and I have no
> explicit waters in my system...
>
> Thanks for your proposition for using xmin but I have a problem when I try
> to run the following input file with AMBER 9:
>
> &cntrl
> imin=1, maxcyc=150000, ntmin=3,
> drms=0.05, ntb=0,
> cut=12.0, ntpr=100,
> &end
>
> In the output file, I have an error message:
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> LMOD XMIN Minimization.
> ERROR: LMOD XMIN is unavailable.
>
> Do you know is wrong with that??
>
> Thanks once more
>
> Daniel
>
>
> David A. Case wrote:
>
>> On Thu, Feb 12, 2009, Daniel Emery wrote:
>>
>>
>>> I performed a 5ns MD with sander on a system with about 30'000 atoms and
>>> no periodic conditions.
>>> Everything it's fin along the dynamic.
>>> After that I extract, with ptraj, the average structure of the last 50ps
>>> of the MD.
>>> I try to optimize this structure and I give a drms at 0.05. But the RMS
>>> don't converge to this value. I have a minimum value at something like
>>> 0.2...
>>>
>>>
>>
>> You don't say how many minimization steps you used, or whether or not
>> you have explicit waters. It can take many tens of thousands of steps
>> to minimize to a low rms for 30,000 atoms. The xmin minimizer will
>> generally do a better job than conjugate gradients, so you might try
>> that.
>>
>> ...dac
>>
>>
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>>
>>
>>
>
> --
> EMERY Daniel
> Ph.D. Student (Lab. R1)
> Department of Organic Chemistry
> University of Geneva
> 30, quai Ernest-Ansermet
> CH-1211 Geneva 4
> +41 22 379 61 55
>
>
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Received on Fri Feb 13 2009 - 01:19:04 PST
