From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Aug 05 2016 - 02:46:00 CDT
Hi Emerson,
To add to Jérôme's comment: an MD code that's meant to be more flexible
(ie, easier to extend), might suit you better. Did you take a look at OpenMM
<http://openmm.org/>? Costom forces should be easier to implement
<http://docs.openmm.org/7.0.0/userguide/theory.html#customnonbondedforce>.
Best,
Ajasja
On 5 August 2016 at 00:21, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> Hi Emerson,
>
> Based on your description, and for the reasons Brian mentioned, NAMD is
> probably not the right software for your project.
>
> Jerome
>
> On 4 August 2016 at 22:17, Brian Radak <bradak_at_anl.gov> wrote:
>
>> 1.) I'm not sure you can turn off the computation of electrostatics
>> completely, but using "PME off" should bypass a lot of the computational
>> cost. You can turn off the effect of electrostatics in a number of ways,
>> for example by zeroing the charges or just using "nonbondedscaling 0", but
>> the latter also turns of LJ interactions I believe.
>>
>> 2.) TclForces is a good sandbox for trying new models, but I wouldn't
>> necessarily recommend it for production runs of something like brute force
>> protein folding.
>>
>> If you are doing pairwise potentials, you can also try using the
>> tabulated non-bonded interactions, but these might not be well-typed for
>> what you want.
>>
>> Unfortunately (fortunately?) the main purpose of NAMD is exactly to
>> accelerate the electrostatics, so those routines are a pretty essential and
>> central part of normal execution. You'd have to tell use more about what
>> kinds of models you want to use to get more specific advice.
>>
>> HTH,
>> Brian
>>
>>
>> On 08/04/2016 01:15 PM, Emerson Macedo wrote:
>>
>>> Hello NAMD experts!!
>>>
>>> I am new with NAMD and currently working on
>>> adapt it to our research with proteing folding simulations.
>>>
>>> My current challenge involves the possibility of using our
>>> implementation of electrostatic force calculations instead of NAMD's
>>> version.
>>>
>>> My first thought was (naive I guess) find a way to
>>> disable NAMD version and then add out implementation.
>>>
>>> Here my questions:
>>>
>>> 1) How does one could disable NAMD electrostatic calculations or replace
>>> them?
>>>
>>> 2) Does it make sense to use TCLForces API to implement our version or
>>> would be
>>> better to implement directly in the source code?
>>>
>>>
>>> Any directions would be very much appreciated.
>>> Thank you all for any help.
>>>
>>>
>>> My best regards,
>>>
>>> Emerson
>>>
>>>
>> --
>> Brian Radak
>> Postdoctoral Appointee
>> Leadership Computing Facility
>> Argonne National Laboratory
>>
>> 9700 South Cass Avenue, Bldg. 240
>> Argonne, IL 60439-4854
>> (630) 252-8643
>> brian.radak_at_anl.gov
>>
>>
>
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