[gmx-users] Re: grompp for minimization: note & warning

[Tsjerk Wassenaar]

Hi Shahab,

What did you do exactly? Can you state your complete protocol (1. fetched
this structure file there, 2. got the topology from there, 3. did
something, 4. ran grompp like this, etc)? Use brief, clear explanations and
the command lines as you issued them.

Cheers,

Tsjerk


On Tue, Sep 17, 2013 at 2:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/17/13 8:47 AM, shahab shariati wrote:
>
>> Dear Justin
>>
>> Very very thanks for your quick reply.
>>
>> I am very confused and amazed.
>>
>> After visualization of atom 618 ( where the maximum force is),
>> what should I do to resolve me problem.
>>
>> Any help will highly appreciated.
>>
>>
> I honestly have no idea.  There's something nasty going on there, but only
> you have the ability to see it.  You can always try a smaller value of
> emstep, a different EM algorithm, etc.  Try setting nstxout = 1 and
> visualize the entire EM "trajectory" to see where things start to go out of
> control.  And finally, if it really isn't working, ask the people who
> provided the coordinates - they're supposed to be pre-equilibrated, so if
> you can't get it to minimize, maybe there's something wrong that's happened
> before you even got your hands on the file.
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> University of Maryland, Baltimore
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>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
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-- 
Tsjerk A. Wassenaar, Ph.D.