From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Sun Sep 28 2014 - 13:06:06 CDT
No. Large harmonic restraints (i.e. large enough to mostly prevent a bond
from stretching) would cause *exactly* the same integration time step
issue as large bond force constants; to the integrator, there's no
difference. We just had this whole discussion less than a month ago;
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/3241.html
The NAMD developers didn't react that time, and neither did they on an
earlier closely related thread, so I'm henceforward going to assume it is
not possible to define rigidBonds between heavy atoms, meaning you'll have
to use a different simulation software. If so, dear NAMD developers, I
myself have absolutely nothing to gain from it, but there does seem to
exist a certain demand for rigidBonds between heavy atoms...
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/3072.html
On 09/28/2014 07:50 AM, Mike Makowski wrote:
> Javad,
>
> Harmonic restraints are your best bet. You'll have to include parameters in
> your CHARMM FF parameter file and also in your NAMD config file. See this
> CHARMM documentation:
>
> http://www.charmmtutorial.org/index.php/Essential_CHARMM_Features#Harmonic_restraints
>
> They explain how to keep a residue rigid.
>
> Mike
>
> Michael Makowski
> University of California, Irvine
> Department of Chemistry,
> Chemical and Material Physics,
> Irvine, CA 92617
> Cell: 267 588 9865
> Office: 949 824 5776
>
>
>
> On Sun, Sep 28, 2014 at 4:02 AM, Javad Noroozi <noroozi_javad_at_ymail.com>
> wrote:
>
>> Mike,
>>
>> First, what you mean by incorrect assumptions?
>>
>> TraPPE and CHARMM use the same functional form for non-bonded and some
>> bonded(bonds and bending) potentials. So,one can convert the parameters
>> between the two force fields.The problem is that TraPPE use rigid bonds
>> which is equivalent to very large spring constant in harmonic potentials. I
>> want to know if there is any way to handle the rigid bonds in NAMD similar
>> to virtual sites used in Gromacs tutorial?
>> To my knowledge,the SHAKE algorithm implemented in NAMD works for water
>> molecules only.
>>
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html
>>
>> Bests,
>> JAVAD
>>
>>
>> _____________________
>> Javad Noroozi,Department of Chemical Engineering,Sharif University of
>> Technology
>> Email: jnoroozi_at_che.sharif.ir
>>
>>
>>
>>
>>
>>
>> ________________________________
>> From: Mike Makowski <mmakowsk_at_uci.edu>
>> To: Javad Noroozi <noroozi_javad_at_ymail.com>
>> Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
>> Sent: Sunday, 28 September 2014, 11:33:10
>> Subject: Re: namd-l: Molecular Dynamics of Rigid Linear Molecules in NAMD
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