[gmx-users] LINCS

[Justin A. Lemkul]

teklebrh at ualberta.ca wrote:
> Hi Justin,
> 
> "There is something physically unrealistic about your model"
> 
> You are right!
> 
> The main problem I found out is that some of the structures in my 
> Solution broke down......
> 
> I used ...
> 
> genbox -cp XXXX.grob -nmol 20 -ci insert.gro -cs spc216.gro XXX.top 
> -XXXXXX.gro
> 
> To generate multiple structures in a box. However, it creates overlap 
> and my orginal structures broke down. I checked the structures!
> 

Using -ci and -cs simultaneously typically breaks down.  Use -ci to add your 
molecules, then in a separate step, use -cs to solvate the box.

-Justin

> Can you please let me how to generate multiple structures in a fixed box 
> at random or packed in a solutio (e.g water)
> 
> Thank you for you help
> 
> Robella
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
>>
>>
>> teklebrh at ualberta.ca wrote:
>>> Hi Justin,
>>>
>>> I tried to run full MD after energy minimization in both vacuo and 
>>> water... went good but I got this ERROR once I try to run full MD.
>>>
>>> Can you please help.....
>>
>> There is something physically unrealistic about your model.  That's 
>> the case whenever you see a LINCS warning.  Without a more complete 
>> description of what you've done (minimization and equilibration 
>> protocol, initial construction of the model, etc) and the details of 
>> your simulation parameters, there's nothing more anyone can really say 
>> beyond a guess.
>>
>> It appears that the wiki is down at the moment, but these pages have 
>> useful information (when the site comes back up):
>>
>> http://oldwiki.gromacs.org/index.php/blowing_up
>> http://oldwiki.gromacs.org/index.php/Errors
>>
>> And since LINCS errors have been posted thousands of times to the 
>> list, the archive should have some useful advice as well, so search here:
>>
>> http://oldwww.gromacs.org/swish-e/search/search2.php
>>
>> -Justin
>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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