What I am most intrigued here is, I have ~4 million atoms of solute and
leap takes ~1 hour to read the pdb and create the prmtop and inpcrd files
Whereas for the similar number of water molecules, leap is ~50 times slower
in creating the input files.
Note: I stripped hydrogen and kept only oxygen atoms in the pdb file before
loading
ATOM ***** O WAT 7160745 -179.864 8.554 -13.358 1.00 0.00 A
TIP
ATOM ***** O WAT 7160746 37.736-113.528-227.411 1.00 0.00 A
TIP
Am I missing something basic here.
Sincerely
Himanshu
On Fri, Feb 7, 2020 at 11:08 AM Himanshu Joshi <himanshuphy87.gmail.com>
wrote:
> Dear Prof Case,
>
> Thanks for your response, I will appreciate if you can suggest any
> possible get around.
>
> There are solutes like DNA, protein and counterions in the system, I am
> using parmbsc1 and ff14 for the DNA and protein, tip3p for water model.
> However, the time consuming part is the water in the system,
>
> One update, the tleap proceeding becomes even slower as the time
> proceeds, contrary to earlier estimate, after 12 hours it has created only
> 500,000 water
> molecules. And now I am concerned that it might be slower towards the
> end.
>
> Thank you.
> Sincerely
> Himanshu
>
>
>
>
>
> On Fri, Feb 7, 2020 at 7:00 AM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Thu, Feb 06, 2020, Himanshu Joshi wrote:
>> >
>> >Although, I could manage to tweak the pdb file format to get recognized
>> by
>> >tleap but the process of generating the topology and coordinate file is
>> >slower, (approximately 12 hours for 1 million atoms).
>>
>> What force fields are you using? Is this just pure water, or are there
>> solutes?
>>
>> I've seen behavior that sounds similar, but I'm trying to narrow down
>> when it happens. No promises, however, that there will be any easy fix
>> or workaround.
>>
>> ...dac
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
>
> *With Regards,HIMANSHU JOSHI *
>
--
*With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
TheoryDepartment of Physics IISc.,Bangalore India 560012*
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Received on Fri Feb 07 2020 - 12:30:02 PST
