As Bill says you could try running a very low temp 10k md run with pmemd or pmemd.cuda with the inpcrd from leap.
On 05/04/2016, 10:26, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
>For what it's worth, md at e.g. 10K can energy minimize a system better
>than simple energy minimization.
>
>Bill
>
>On 4/5/16 2:16 AM, TERREUX RAPHAEL wrote:
>> Sorry... the exact number is the one in inpcrd files.... I have no problem with pmemd....
>>
>> My problem is how to minimize the system prior uses pmemd.
>>
>>
>>
>> -----Message d'origine-----
>> De : Gould, Ian R [mailto:i.gould.imperial.ac.uk]
>> Envoyé : mardi 5 avril 2016 11:13
>> À : AMBER Mailing List
>> Objet : Re: [AMBER] sander number of atoms limit
>>
>> Dear Raphael,
>>
>> We routinely run systems which are greater than 1M atoms, currently our largest is 1.8M atoms, we run these on the cuda version of pmemd. You say in your e-mail that the size is exactly 1,149,859 however you inpcrd says 1,158,949 which is bigger and I think this is your problem with sander. Check that your number of atoms in the parm file you are using matches the number of atoms in the inpcrd.
>>
>> Cheers,
>> Ian
>>
>> --
>> Dr Ian R Gould, FRSC.
>> Reader in Computational Chemical Biology Department of Chemistry Imperial College London Exhibition Road London
>> SW7 2AY
>> E-mail i.gould.imperial.ac.uk
>> http://www3.imperial.ac.uk/people/i.gould
>> Tel +44 (0)207 594 5809
>>
>>
>>
>>
>>
>>
>>
>>
>> On 05/04/2016, 09:59, "TERREUX RAPHAEL" <raphael.terreux.univ-lyon1.fr> wrote:
>>
>>> Hi,
>>>
>>> I am trying to make a MD of a large system which exceed 1 M atoms (1,149,859 exactly). I used sander just for minimizing the system before used pmemd.
>>> If pmemd and pmemd.cuda has a limit to few millions atoms, sander or its file format used seems to have 999.999 atoms limits.
>>> When the minimization ended the first two lines of the crd files are changed from :
>>>
>>> default_name
>>> 1158949
>>> 80.3846739 199.1308729 115.0638892 79.5031396 199.3859663 114.6420770
>>> ...
>>>
>>> To
>>>
>>> defa
>>> ******
>>> 80.8650585 199.3545504 114.9412061 79.8759488 199.6309180 114.8514299
>>> ...
>>>
>>> Imin=1 seems not work on pmemd (which is logical)
>>> How could minimize a system with more than 1M atoms on amber 14/ambertools 15
>>> Thanks in advances
>>>
>>> Raphael Terreux
>>>
>>>
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Received on Tue Apr 05 2016 - 03:00:04 PDT
