Re: Wtrlt: Smeart out 9/3 LJ wall

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Wed Jul 15 2009 - 12:21:09 CDT

Hi Sabine,

The other option if TclBC is too cumbersome or slow is to go in and
hard code something into NAMD. Search for GlobalMasterMisc in the
source for an example. I haven't looked at the new namd 2.7 source to
see if this is still and available option or if there is a cleaner
way, but this was a decent solution that I used with 2.6.

Josh

On Jul 15, 2009, at 10:10 AM, Axel Kohlmeyer wrote:

> On Wed, 2009-07-15 at 14:48 +0200, Sabine Leroch wrote:
>>
>>
>>>>> Sabine Leroch 7/13/2009 2:36 PM >>>
>>
>>
>> Dear all
>
> dear sabine,
>
>
>> I am new to NAMD, as I found nothing related in the mailing list, I
>> have to post following question. I need to simulate the adsorption of
>> aminoacids in water at a graphite wall. As it is computationally very
>> costly to use an atomic graphite slide, I want to represent the wall
>> by a smeart out Steele 9/3 LJ potential. Is this possible with NAMD?
>> If yes, how can I set the command in the input file?
>
> not sure how to do this in detail, but my guess would be to try out
> the Tcl Boundary Forces (TclBC) facility. check out the NAMD user's
> guide. perhaps there may also be some examples in the NAMD tutorials
> somewhere.
>
> cheers,
> axel.
>
>
>>
>>
>> Thank you very much
>>
>>
>> Best regards
>>
>> Sabine
>>
>
> --
> =
> ======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
> www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =
> ======================================================================
> If you make something idiot-proof, the universe creates a better
> idiot.
>

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