.@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of
> Alessandra Villa
> Sent: maandag 17 februari 2020 9:34
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Tabulated potentials
>
> Hi,
> On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari <
&g
sandra Villa
> Sent: donderdag 13 februari 2020 16:28
> To: gmx-us...@gromacs.org; gromacs.org_gmx-users <
> gromacs.org_gmx-users@maillist.sys.kth.se>
> Subject: Re: [gmx-users] Tabulated potentials
>
> Hi,
>
> On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari <
> ali.kho
ebruari 2020 16:28
> To: gmx-us...@gromacs.org; gromacs.org_gmx-users <
> gromacs.org_gmx-users@maillist.sys.kth.se>
> Subject: Re: [gmx-users] Tabulated potentials
>
> Hi,
>
> On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari <
> ali.khoday...@student.kuleuven.be> w
,
Ali
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Alessandra
Villa
Sent: donderdag 13 februari 2020 16:28
To: gmx-us...@gromacs.org; gromacs.org_gmx-users
Subject: Re: [gmx-users] Tabulated potentials
Hi,
On Wed, Feb 12, 2020 at 10:59 PM
Hi,
On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari <
ali.khoday...@student.kuleuven.be> wrote:
> Dear Gromacs users,
>
> I’ve got a question regarding the tabulated potentials for bonded
> interactions.
>
> Gromacs recognises and reads the non-bonded potential tables through the
> energy groups s
Dear Gromacs users,
I’ve got a question regarding the tabulated potentials for bonded interactions.
Gromacs recognises and reads the non-bonded potential tables through the energy
groups specified. But how can I refer each bond type to its table?
I have derived coarse-grained potentials for a c
Best,
>
> Zhengcai
>
>
>
> Date: Sat, 23 May 2015 11:55:22 +
> From: Mark Abraham
> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Tabulated potentials
> Message-ID:
>
> Content-Type: text/plain; charset=UTF-
Hi,
Does your table reproduce the potential and force for two methane atoms at
different distances (use mdrun -rerun)
Mark
On Sat, May 23, 2015 at 1:21 PM 张正财 wrote:
> Dear all,
> I want to add the Morse potential (
> U=D*[exp(a*(1-r/r0)-2*exp(a/2*(1-r/r0)] ) for nonbonded interactions
Dear all,
I want to add the Morse potential (
U=D*[exp(a*(1-r/r0)-2*exp(a/2*(1-r/r0)] ) for nonbonded interactions between
CH4-CH4. So, I made three table files to correspond to the interactions between
H-H, C-H, and C-C, and I changed vdwtype=user ,Dispcorr=no , energrps = C H ,
and en
Dear GROMACS users and developers, I am using GROMACS 5.0.1.
I would like to use tabulated potentials (Aziz ones for argon and krypton in
particular); as a starting test, I began with LJ tabulated potential. I
followed the instructions on the manual, and I did well because my .xvg file of
Lenn
Thanks for pointing me to this, this could actually work.
Cheers
Sabine
Am 05.05.2014 16:05, schrieb Mark Abraham:
I've no idea whether PME-User (read its description!) and enerygrp-table
interact in a way useful to you, but it might. You were going to test
whether your implementation of your
I've no idea whether PME-User (read its description!) and enerygrp-table
interact in a way useful to you, but it might. You were going to test
whether your implementation of your model was working correctly anyway,
right? ;-)
Mark
On Mon, May 5, 2014 at 1:25 PM, Sabine Reisser wrote:
> But I ca
But I cannot have specific interactions between two groups and normal
PME for the rest, right?
Cheers
Sabine
Am 05.05.2014 10:41, schrieb Mark Abraham:
On May 5, 2014 10:01 AM, "Sabine Reisser" wrote:
So that means the electrostatics are calculated as given in the tables
and no long range
On May 5, 2014 10:01 AM, "Sabine Reisser" wrote:
>
> So that means the electrostatics are calculated as given in the tables
and no long range electrostatics corrections (like PME or RF) are applied?
Correct. The .mdp settings determine what interactions are computed; the
table just says the value
So that means the electrostatics are calculated as given in the tables
and no long range electrostatics corrections (like PME or RF) are applied?
Cheers
Sabine
Am 28.04.2014 18:28, schrieb Justin Lemkul:
On 4/28/14, 9:19 AM, Sabine Reisser wrote:
Hi,
I'm using tabulated potentials to creat
On 4/28/14, 9:19 AM, Sabine Reisser wrote:
Hi,
I'm using tabulated potentials to create a hole in a membrane. I define three
groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For the
interactions between the dummy atoms and the hydrophobic chains I define an
exclusively repulsive
Hi,
I'm using tabulated potentials to create a hole in a membrane. I define
three groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For
the interactions between the dummy atoms and the hydrophobic chains I
define an exclusively repulsive potential. All other interactions are
defi
On Tue, Jan 21, 2014 at 1:45 PM, Mark Abraham wrote:
> Tabulated, yes. With all algorithms, who knows? Tabulated non-bondeds on
> GPU, I highly doubt. GPUs are for computing, not looking up random-access
> tables.
Actually, the CUDA Ewald non-bonded kernels are tabulated on Fermi
GPUs - the textu
Tabulated, yes. With all algorithms, who knows? Tabulated non-bondeds on
GPU, I highly doubt. GPUs are for computing, not looking up random-access
tables.
Mark
On Tue, Jan 21, 2014 at 12:19 PM, Steven Neumann wrote:
> Dear Gromacs Users,
>
> Can you please write me whther Gromacs 4.6 support tab
Dear Gromacs Users,
Can you please write me whther Gromacs 4.6 support tabulated potentials for
bonded and non-bonded interactions?
Steven
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