On Thu, Aug 29, 2013 at 7:18 AM, Gianluca Interlandi
wrote:
> Justin,
>
> I respect your opinion on this. However, in the paper indicated below by BR
> Brooks they used a cutoff of 10 A on LJ when testing IPS in CHARMM:
>
> Title: Pressure-based long-range correction for Lennard-Jones interactions
On 8/29/13 6:23 PM, Gianluca Interlandi wrote:
And interestingly, they point out at differences between the various
implementations of the switching function. Also, when trying to replicate the
CHARMM energies, the authors did not use any cutoff at all and performed the
calculations in vacuo. I
And interestingly, they point out at differences between the various
implementations of the switching function. Also, when trying to replicate
the CHARMM energies, the authors did not use any cutoff at all and
performed the calculations in vacuo. If you look at Table 1 in the paper,
it is exact
Yes, I've seen that thread before. My feeling is that simulating membranes
with the CHARMM36 FF is a different story. It's good to be aware of that.
Gianluca
On Thu, 29 Aug 2013, Justin Lemkul wrote:
On 8/29/13 5:15 PM, Gianluca Interlandi wrote:
Of course, if accuracy is not in question th
On 8/29/13 5:33 PM, Gianluca Interlandi wrote:
And also, gromacs does not seem to use the same switching function as CHARMM.
Has it been tested how much this affects replication of the original CHARMM MM
energies?
Yes.
dx.doi.org/10.1021/ct900549r
-Justin
--
==
And also, gromacs does not seem to use the same switching function as
CHARMM. Has it been tested how much this affects replication of the
original CHARMM MM energies?
Gianluca
On Thu, 29 Aug 2013, Gianluca Interlandi wrote:
Of course, if accuracy is not in question then performance dominates.
On 8/29/13 5:15 PM, Gianluca Interlandi wrote:
Of course, if accuracy is not in question then performance dominates. I have
seen countless reports on this list and elsewhere where small changes in
cutoffs lead to wildly incorrect behavior, affecting every force field. Thus,
I am always extreme
Of course, if accuracy is not in question then performance dominates. I have
seen countless reports on this list and elsewhere where small changes in
cutoffs lead to wildly incorrect behavior, affecting every force field.
Thus, I am always extremely skeptical of such changes. The effects can b
On 8/29/13 2:52 PM, Gianluca Interlandi wrote:
That's good to know that you've tested different setups. Are the water
interaction energies comparable? Have you tested model compounds or just full
proteins? Over how long of a time period?
I have tested only full proteins over a 50-ns period
That's good to know that you've tested different setups. Are the water
interaction energies comparable? Have you tested model compounds or just
full proteins? Over how long of a time period?
I have tested only full proteins over a 50-ns period. I have not
calculated yet the water interactio
IPS in CHARMM involves additional calculations beyond a simple
homogeneous approximation -- roughly equivalent to PME for dispersion,
though its a bit messier.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723858/
On Thu, Aug 29, 2013 at 7:56 AM, Justin Lemkul wrote:
>
>
> On 8/29/13 1:18 AM, G
On 8/29/13 1:18 AM, Gianluca Interlandi wrote:
Justin,
I respect your opinion on this. However, in the paper indicated below by BR
Brooks they used a cutoff of 10 A on LJ when testing IPS in CHARMM:
Title: Pressure-based long-range correction for Lennard-Jones interactions in
molecular dynami
Justin,
I respect your opinion on this. However, in the paper indicated below by
BR Brooks they used a cutoff of 10 A on LJ when testing IPS in CHARMM:
Title: Pressure-based long-range correction for Lennard-Jones interactions
in molecular dynamics simulations: Application to alkanes and inte
On 8/28/13 9:09 PM, Gianluca Interlandi wrote:
Current CHARMM development relies on a 1.2-nm cutoff for LJ, so that's how we
balance all of the forces during parameterization.
Ok, I agree. What about the use of PME for Coulomb? The CHARMM PARAM22 force
field was parametrized using SHIFT on el
Current CHARMM development relies on a 1.2-nm cutoff for LJ, so that's
how we balance all of the forces during parameterization.
Ok, I agree. What about the use of PME for Coulomb? The CHARMM PARAM22
force field was parametrized using SHIFT on electrostatic forces making it
zero after 12 A (pl
On 8/28/13 7:28 PM, Gianluca Interlandi wrote:
Thanks for your replies, Mark. What do you think about the current DispCorr
option in gromacs? Is it worth it trying it? Also, I wonder whether using
DispCorr for LJ + PME for Cb justifies reducing the cutoff for non-bonded to 1
nm with the CHARMM
Thanks for your replies, Mark. What do you think about the current
DispCorr option in gromacs? Is it worth it trying it? Also, I wonder
whether using DispCorr for LJ + PME for Cb justifies reducing the cutoff
for non-bonded to 1 nm with the CHARMM force field, where 1.2 nm is
usually recommende
Secondarily, one could use the same cut-off for LJ and electrostatics,
and treat their respective lattice components however you like. This
simplifies implementations for computing short-ranged interactions,
while facilitating iso-accuracy load balancing across heterogeneous
compute units.
Mark
O
On 2013-08-28 09:31, rajat desikan wrote:
Hi,
What is LJ PME? I googled it and got this publication?
http://pubs.acs.org/doi/abs/10.1021/ct400146w
So, LJ will not be cut off at some r, but you will have a real+fourier part
similar to electrostatics. Is that LJ PME? What are the advantages?
htt
Hi,
What is LJ PME? I googled it and got this publication?
http://pubs.acs.org/doi/abs/10.1021/ct400146w
So, LJ will not be cut off at some r, but you will have a real+fourier part
similar to electrostatics. Is that LJ PME? What are the advantages?
On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham
Lennard-Jones PME is planned for 5.0
Mark
On Aug 28, 2013 8:36 AM, "Gianluca Interlandi"
wrote:
> Hi!
>
> Just wondering whether gromacs has (or plans to implement) a correction
> for the loss of long range LJ interactons? Something similar to
> LJcorrection in NAMD or IPS in CHARMM.
>
> Thanks!
DispCorr might be what you are looking for, correction for LJ beyond the
cut-off.
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
--
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