I forgot to attached this to the last email. To get single outputs along a
trajectory use imin=5
On Tue, Jun 1, 2010 at 4:21 PM, Dwight McGee <dwight.mcgee.gmail.com> wrote:
> Hi,
>
> To answer your first question: Delphi can't be run on more than one
> processor. It can be made quasi-parallel by sending each snapshot to its own
> processor and I believe the mm_pbsa.pl released in amber11 should have
> this capability.
>
>
> On Tue, Jun 1, 2010 at 3:55 PM, Yuqin Cai <yuqin.cai.2008.gmail.com>wrote:
>
>> Dear AMBER community,
>>
>> I am computing free energies for three carcinogen-containing duplexes
>> using
>> MM-PBSA. By replacing the carcinogen with a hydrogen atom, i can compare
>> the
>> distortion each carcinogen causes to the B-DNA duplex. Here are my
>> questions:
>>
>> 1) how to use multiple processes, especially during delphi? For an 800
>> atom
>> structure, it took me ~2 weeks to get the average free energy over 5000
>> snapshots. I wonder if i could make it faster.
>>
>> 2) how to put out the results for each snapshot during the trajectory,
>> instead of an overall average, so that I can do a clustering analyses?
>>
>> 3) how to cap the ends if i want to carry out analyses for a cropped
>> structure?
>>
>> Many thanks,
>>
>> Yuqin
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Tue Jun 01 2010 - 13:30:08 PDT
