t; To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] PME constant shifts.
>
> Hello,
>
> Thanks for the quick reply, I am not sure if you are referring to this term
> of the Ewald Sum:
>
> V_0 = ( f*beta ) * SUM(q_i^2) / sqrt(pi)
>
> Since the sum of the square of the
, March 29, 2019 3:15 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] PME constant shifts.
Hello,
Thanks for the quick reply, I am not sure if you are referring to this term
of the Ewald Sum:
V_0 = ( f*beta ) * SUM(q_i^2) / sqrt(pi)
Since the sum of the square of the charges of the system
Hello,
Thanks for the quick reply, I am not sure if you are referring to this term
of the Ewald Sum:
V_0 = ( f*beta ) * SUM(q_i^2) / sqrt(pi)
Since the sum of the square of the charges of the system (AB) is the same
as the sum of the square of the charges of the system (A) plus the same
from sys
Dear Sergio,
If you're using PME, you need to also include the reciprocal contribution.
Gerrit
Dear gmx comunity,
I am trying to calculate the electrostatic interaction of my system for
force field development. My system consists of 7 positively charged
particles interacting (system A) with
Hi,
The negative energy is due to the uniform background charge that appears when
your system has a net charge, not due to shifting of pair interactions.
Computing the absolute energy of a periodic system with net charge is
meaningless.
Cheers,
Berk
From: gr
Oliver,
I am very grateful for the reply and the additional references. I will
take the suggested Roux, Garcia, and Hünenberger studies into account when
planning new simulations.
Best,
Eric
On Fri, Nov 30, 2018 at 6:53 PM Oliver Beckstein wrote:
> You might also want to look at work from Hum
You might also want to look at work from Hummer, Hünenberger, and recently
Rocklin, Mobley and Hünenberger before you decide that you can neglect the
influence of PME on solvation free energies.
[0] G. Hummer, L. Pratt, and A. Garc ́ıa. Free energy of ionic hydration. The
Journal of Physical C
Justin,
That is encouraging! Thanks for the guidance and the rapid reply.
Best,
Eric
On Fri, Nov 30, 2018 at 12:30 PM Justin Lemkul wrote:
>
>
> On 11/30/18 1:56 PM, Eric Smoll wrote:
> > Hello GROMACS users,
> >
> > In systems that require accounting for long-range electrostatic
> > interact
On 11/30/18 1:56 PM, Eric Smoll wrote:
Hello GROMACS users,
In systems that require accounting for long-range electrostatic
interactions, is there a reasonable MD strategy for calculating the
solvation free energy of individual ions (I am not worried about ion
pairs)? If I use the BAR method
That's the PP-PME load balancing output (see -tunepme option /
http://manual.gromacs.org/documentation/2018/user-guide/mdrun-performance.html
).
--
Szilárd
On Tue, Jul 10, 2018 at 7:35 PM Mahmood Naderan
wrote:
> Hi,
> When I run mdrun with "-nb gpu", I see the following output
>
>
> starting
Hi,
Not directly, and anyway the PME grid only has the long-ranged component of
anything. You could use mdrun -rerun to compute the potential via adding a
new test particle to the system in its own energy group and observing its
energy as you move its position.
Mark
On Wed, Nov 30, 2016 at 7:11
ular Biophysics
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: Wednesday, October 21, 2015 1:08 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] PME on a non-neutral system
On 10/21/15 12:14 PM, Smith, Micholas D. wrote:
Albert,
Hi,
> Albert,
>
> Gromacs won't automatically neutralize the system (as far as I know). If I
> recall being non-neutral doesn't necessarily result in problems, but may
> instead slow your run-time. I am sure someone will correct me if I am wrong.
>
> Old posts suggest that GROMACS does in fact
n Lemkul
Sent: Wednesday, October 21, 2015 1:08 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] PME on a non-neutral system
On 10/21/15 12:14 PM, Smith, Micholas D. wrote:
> Albert,
>
> Gromacs won't automatically neutralize the system (as far as I know). If I
> recall being
On 10/21/15 12:14 PM, Smith, Micholas D. wrote:
Albert,
Gromacs won't automatically neutralize the system (as far as I know). If I
recall being non-neutral doesn't necessarily result in problems, but may
instead slow your run-time. I am sure someone will correct me if I am wrong.
Old post
Albert,
Gromacs won't automatically neutralize the system (as far as I know). If I
recall being non-neutral doesn't necessarily result in problems, but may
instead slow your run-time. I am sure someone will correct me if I am wrong.
-Micholas
===
Micholas Dean Smith, PhD.
Post-
Hi,
Gromacs always calculates full electrostatics at every time step if PME is
used. That means, both the short-range and the long-range Coulomb contribution
of the Ewald sum are updated at every time step.
Carsten
On 19 Jan 2015, at 01:44, asasa qsqs wrote:
> Dear Justin,I studied KALP15 in
tes with anything useful is... your problem.
Mark
Can you let us know if there is any wrong in our inputs for PME?
>
> Thanks!
>
> Tom
>
>
>
>> Message: 5
>> Date: Mon, 12 Jan 2015 18:44:56 +0100
>> From: Mark Abraham
>> To: Discussion list for GROMACS users
On Sat, Jan 10, 2015 at 5:58 PM, Tom wrote:
> Dear GMX and PEM experts,
>
> I am using gromacs 4.6.5. My system is neutral charge (net charge=0).
> I used PME with the following options:
> -
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range
> e
On Mon, Sep 8, 2014 at 11:39 PM, Szilárd Páll
wrote:
> Hi,
>
> By default, there will be no separate PME ranks used with less than
> AFAIR 12 ranks (i.e. the default with small number of ranks is -npme
> 0). Without separate PME ranks (and without GPUs) there is no PP-PME
> load balance to tweak,
Hi,
By default, there will be no separate PME ranks used with less than
AFAIR 12 ranks (i.e. the default with small number of ranks is -npme
0). Without separate PME ranks (and without GPUs) there is no PP-PME
load balance to tweak, so the PME load is not very relevant from
performance optimizatio
On 22 Aug 2014, at 12:48, xiexiao...@sjtu.edu.cn wrote:
> Does anyone know that what the pme ranks mean?
See for example [1] in the section
Multiple-Program, Multiple-Data PME Parallelization.
Best,
Carsten
1. Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. GROMACS 4:
Algorithms
On Sun, Mar 23, 2014 at 6:40 PM, Albert Romano wrote:
>
> Dear list,
> I have noticed the following changelog from Gromacs 4.6.2:
>
>
> --> Added CUDA PME kernels with analytical Ewald correction
>
>
> Does that mean we can now offload PME computation to GPU?
>
No. That refers to short-ranged ke
Not sure where you read that, but generally order 4 is fine. Higher order
does trade more compute for less communication and different communication
pattern, but when and how that might gain is very situational. You would
also want to adjust rtol and rcoulomb for iso-accuracy, which is tricky.
Use
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