On 6/29/12 11:10 AM, massimo sandal wrote:
On 29 Jun 2012 15:09, "Justin A. Lemkul" <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
>
>
>
> On 6/29/12 9:04 AM, massimo sandal wrote:
>>
>>
>> On 29 Jun 2012 14:08, "Justin A. Lemkul" <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
>>
>> >
>> > The settings in my tutorial are for use with OPLS-AA and are thus not
>> suitable for a simulation with CHARMM. Cutoffs and other aspects will be
different.
>>
>> This is interesting. In general, where can you find optimal mdp settings for
>> each force field?
>>
>
> By reading the primary literature for how each force field was derived. The
parameters are only guaranteed to work within the context of correct cutoffs,
electrostatic schemes, neighborlist update interval, water model used, etc. Some
older force fields have been demonstrated to work well with PME even if
originally derived with RF or some other method, but generally the other
settings must adhere to the original parameterization. Some force fields can be
very sensitive to these incorrect settings.
>
>
Yes, I know, but I hoped someone could have put a table online or wrote a book
chapter somewhere about this.
Wouldn't it be nice to create a table of "standard settings" for each forcefield
in the gmx documentation (with lit references of course)?
Well, anyone is welcome to submit anything they feel would be useful... ;)
I have considered this in the past, but have rejected the thought every time it
comes to mind. It would be nice if there was a central repository of such
parameters, but then likely a simulation becomes "do this, not that" with no
required thought from the end user. If you make simulations a black box,
everyone expects them to automatically work without fail.
The other objection I have always had is the continual improvement of the field.
If Gromacs puts out an "official" or "standard" list of what to do, it is
always subject to change and then becomes incumbent upon a Gromacs contributor
to verify its accuracy frequently. My personal fear is that this becomes an
untenable task. Then in the case of an error, someone's whole Ph.D. could go
out the window...
In the end, I think it's always safe to ask the user to do a bit of legwork to
understand the force field he or she wishes to use. The knowledge gained from
an hour of reading will save a lot of potential headaches.
I would reject any attempt to include such information in the manual (lest its
settings become "official"), but if someone wants to put up a wiki page on the
website with clear warnings and disclaimers, they are welcome to do so.
Just my $0.02.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
