FW: editing the code of the non bonded pair potentials

From: Asaf Farhi (asaf.farhi_at_weizmann.ac.il)
Date: Fri Aug 30 2013 - 19:54:45 CDT

Dear all

Thank you very much for your responses. It was very helpful.
I'm trying to simulate solvation of simple molecules such as phenol etc.
I'll check these software.

Dear Dr. Kohlmeyer

I come from another field (physics) and I was not familiar with MD simulations.
I thought that it's simple implementation but now I understand the hirarchy or tradeoff.
I need a relatively simple demonstration.

I really don't want people to do things without credit, just needed some advice.
Sorry. Please don't get annoyed...

Best regards,
Asaf

owner-namd-l_at_ks.uiuc.edu on behalf of Gianluca Interlandi [gianluca_at_u.washington.edu]ReplyReply AllForwardActions
To:
 ovchinnv_at_georgetown.edu
Cc:
 namd-l_at_ks.uiuc.edu
 Saturday, August 31, 2013 2:34 AM
>> Thanks for this link. I'm really curious about mindy. I have downloaded
>> it. Do you know whether it supports the CHARMM CMAP correction?
>
> Looking at the code, it does not, but that would be easy to adapt from the
> NAMD's ComputeCrossterms.C; the more troublesome part is the lack of
> long-range electrostatic treatments.

If one wants to use it in explicit solvent. Otherwise, one would have to
steal the code for GBSA from NAMD. And I bet it's not that trivial either.

Gianluca

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
                     http://healthynaturalbaby.org
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owner-namd-l_at_ks.uiuc.edu on behalf of Victor [ovchinnv_at_gmx.com]Reply All
 Saturday, August 31, 2013 2:20 AM
On 08/30/2013 07:00 PM, Gianluca Interlandi wrote:
> Hi Victor!
>
> Thanks for this link. I'm really curious about mindy. I have downloaded
> it. Do you know whether it supports the CHARMM CMAP correction?
Gianluca,

Looking at the code, it does not, but that would be easy to adapt from
the NAMD's ComputeCrossterms.C; the more troublesome part is the lack of
long-range electrostatic treatments. Just a good MD toy !

Victor

owner-namd-l_at_ks.uiuc.edu on behalf of Gianluca Interlandi [gianluca_at_u.washington.edu]Reply All
 Saturday, August 31, 2013 2:02 AM
Hi Victor!

Thanks for this link. I'm really curious about mindy. I have downloaded
it. Do you know whether it supports the CHARMM CMAP correction? It
probably also doesn't have the latest additions of NAMD like GBSA.
Nonetheless, an excellent starting point!

Gianluca

owner-namd-l_at_ks.uiuc.edu on behalf of Victor [ovchinnv_at_gmx.com]Reply All
 Friday, August 30, 2013 10:38 PM
There's always Mindy. --Victor
http://www.ks.uiuc.edu/Development/MDTools/mindy/license.cgi?files/mindy-1.0.src.tar.gz

Axel Kohlmeyer [akohlmey_at_gmail.com]Reply All
 Friday, August 30, 2013 10:08 PM
On Fri, Aug 30, 2013 at 8:14 PM, Asaf Farhi <asaf.farhi_at_weizmann.ac.il> wrote:
>
> ________________________________________
> From: Asaf Farhi
> Sent: Friday, August 30, 2013 9:14 PM
> To: Axel Kohlmeyer
> Subject: RE: namd-l: editing the code of the non bonded pair potentials
>
> Thank you very much for the reponse.
> I didn't know that the code is that complex.

what is simple or not depends a lot on your expectations, your skills,
and your experience. the *method* of classical MD *is* simple, but the
implementation may not always mirror that. particularly, lots of
features and good parallel performance come at a price.

> I thought that it is simple and that these places in the code can be easily spotted.

this kind of statement is quite irritating. it means that either you
have not done your due diligence and properly informed yourself about
NAMD before deciding to work on it, or it means that your attitude
towards asking people for help is even worse that it appeared in your
previous post (i.e. that you are just looking for somebody that does
the thinking and work for you and voluntarily lets you have credit as
well).

axel.

> Sorry.
>
> Best regards,
> Asaf
> ________________________________________

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
owner-namd-l_at_ks.uiuc.edu on behalf of Joshua Adelman [jla65_at_pitt.edu]Reply All
 Friday, August 30, 2013 10:07 PM
You might want to take a look at OpenMM (https://simtk.org/home/openmm) if you want to mess around with how forces are being calculated. They have a number of nice facilities for specifying custom forces, integrators, etc and their python interface makes it simple to prototype simulation protocols. I don't know about Asaf's particular use-case, but here is an example of how to code up aMD in OpenMM for example:
https://simtk.org/svn/pyopenmm/trunk/simtk/pyopenmm/extras/amd.py
Cheers,
Josh
owner-namd-l_at_ks.uiuc.edu on behalf of Axel Kohlmeyer [akohlmey_at_gmail.com]Reply All
 Friday, August 30, 2013 10:01 PM
On Fri, Aug 30, 2013 at 8:47 PM, Kenno Vanommeslaeghe
<kvanomme_at_rx.umaryland.edu> wrote:
> On 08/30/2013 10:10 AM, Axel Kohlmeyer wrote:
>
> Axel, sorry for going a bit on a tangent here, but purely out of educational
> interest, can you give a pointer to one (or more) from the top of your head?
depends on what kind of system you want to simulate.
if you just want a toy MD code for simple single type lennard-jones
system with nve verlet integrator, you can easily write one yourself
based on what several books on MD suggest. i wrote one myself for
teaching optimizing and parallelizing a scientific code (and an LJ MD
has about the smallest and simplest compute kernel around that you can
compare to a real life application).
https://sites.google.com/site/akohlmey/software/ljmd
> A quick Google search turned up toyMD, but since you appear to be more
> knowledgeable in these things than I am, I'd like to know your opinion.
if you are looking for something more serious and applicable for read
world simulations, i would suggest something like Tinker or LAMMPS or
a toolkit like ASE or OpenMM.
axel.
> Cheers,
>
>         Kenno.
>
-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
owner-namd-l_at_ks.uiuc.edu on behalf of Asaf Farhi [asaf.farhi_at_weizmann.ac.il]Reply All
Inbox, Sent ItemsFriday, August 30, 2013 9:56 PM
Thank you very much!
I'll look for switching function.
Will be happy to hear the future recommendations.
Best,
Asaf

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