[gmx-users] None constraints and l-bfgs.

[Justin Lemkul]

On 8/9/15 1:17 PM, Dawid das wrote:
> I hope speedy share is fine.
>
> http://www.speedyshare.com/k2YEr/ribonucl-no-constr.tar.gz
>

Works for me with the latest GROMACS.  Are you using some old version?  Note 
that your cutoff setup is wrong for CHARMM force fields.  See 
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

-Justin

> 2015-08-09 18:08 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 8/9/15 11:40 AM, Dawid das wrote:
>>
>>> Dear Justin,
>>>
>>> I still have problems with performing l-bfgs minimization.
>>> I use
>>>
>>> constraints              = none ; no constraints
>>> define                   = -DFLEXIBLE
>>>
>>> in my *mdp file and in *top file there is nothing related to constraints.
>>> I still get this error that l-bfgs and constraints are not implemented.
>>> What am I missing?
>>>
>>>
>> Without seeing your files, no clue.  Upload a tarball of all your inputs
>> (.mdp, topology(ies), coordinates) to a (non-spammy) file-sharing service
>> and I'll take a look.
>>
>> -Justin
>>
>> Dawid Grabarek
>>>
>>>
>>> 2015-07-29 13:32 GMT+01:00 Dawid das <addiw7 at googlemail.com>:
>>>
>>>
>>>> 2015-07-29 12:36 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>>>>
>>>> To turn that off you would need "define = -DFLEXIBLE" but you should
>>>>> subsequently re-minimize with constraints to avoid weird geometries.
>>>>>
>>>>
>>>>
>>>>
>>>> I forgot about it. Thank you!
>>>>
>>>> Dawid Grabarek
>>>>
>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================