Hello Users,
Recently I have been trying to implement the use of tabulated potentials in
GROMACS to an system of argon atoms.
I run a NVE simulation of 1000 argon atoms and then plot the potential energy
from the output.
ar.itp :
[ defaults ]
; nbfunccomb-rule gen-pairs fu
Hi,
i meant to perform a free energy calculation to get the chemical
potential of water, and made a number of input files based on the excellent
tutorial
by Justin Lemkul.
(Without thinking) I also tried using a tabulated potential for electrostatics
with: coulombtype = User
but it seems to wor
Dear Mark,
I am very Thankful to you for your valuable suggestion.
On Thu, Jun 7, 2012 at 12:04 PM, Mark Abraham wrote:
> On 7/06/2012 4:33 AM, ramesh cheerla wrote:
>
> Dear Mark,
>
> Thank you for your reply, According to my
> understanding functional form of di
On 7/06/2012 4:33 AM, ramesh cheerla wrote:
Dear Mark,
Thank you for your reply, According to my
understanding functional form of dihedral function type 9 is same as
dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except
the difference that function type 9 i
Dear Mark,
Thank you for your reply, According to my
understanding functional form of dihedral function type 9 is same as
dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except the
difference that function type 9 is used to handle the multiple potential
functions
On 4/06/2012 3:46 AM, ramesh cheerla wrote:
Dear Gromacs experts,
I am planing to use tabulated
potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos
n(phi-phi0)] , Here 1<= n <= 3 . I have three different K values (i.e
K1,K2,K3 ) one for eac
Dear Gromacs experts,
I am planing to use tabulated potentials
for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] ,
Here 1<= n <= 3 . I have three different K values (i.e K1,K2,K3 ) one for
each 'n' value ( Here 'n' is multiplicity). I have
Dear Gromacs users,
I am using tabulated potentials for the dihedrals
of my system, the dihedral function I am using is Summn over 'n' 0.5*K [
( Cos n(phi-phi0)] , Here 1<= n <= 3 .
The C-O-C-C dihedral of my system has three folds those are n= 1 , 2, 3
and three diff
Dear Gromacs users,
I am using tabulated potentials
for dihedrals of my system which is of form dih = (1/2)*K[COS
n(phi-phi0)], Here n=3.
I have generated table_d0.xvg by uniformly varying "phi" as 0.1 from -180
to 180 and calculated the numerical derivat
All,
I'm simulating a very small system of methane using tabulated
potentials. Charges are not modified and I'm using a cubic for values up
to 0.19 nm and the normal 6-12 LJ potential after that (the form the
cubic is such that the value and gradient at 0.19 nm is the same as for
the 6-12 LJ).
Hi
I want to try out different potentials using tabulated potential method. I
am planning to specify sigma and epsilon such that C6 and C12 values will be
1.0 and in table.xvg file 6th and 7th columns will contain actual potential
and force values, whereas columns 2-5 will be zero.
As per manua
Hi
Is it possible to use use specified potentials only for vdw type non-bonded
interactions while keeping usual PME,bonded, pairs interactions?
When I specifiy "User" for vdwtype force in .mdp file, I am observing that
mdrun expects table for bonded interactions also through -tableb option and
by
- Original Message -
From: Gareth Tribello
Date: Thursday, September 16, 2010 4:33
Subject: Re: [gmx-users] Tabulated potentials and normal nonbonded interaction
at the same time
To: Discussion list for GROMACS users
> Hello
>
> I think what you need to do is use multip
Hello
I think what you need to do is use multiple tables. So you have one
table for your CG-solvent interaction with itself and then another one
for your CG-solvent (uncharged) interactions. (This second table
would then just a tabulated version of the Lennard Jones interaction
or whatever you a
Dear Gromacs-User,
i want to try to simulate an atomistic molecule with CG-solvent
(uncharged). For the atomistic molecule i want to use the normal
non-bonded interactions, but for the CG-solvent interaction with itself
and the molecule i need a tabulated potential.
So my question is, is that
Hi guys,
>From what I've tested, it seems that performances decreases linearly with
the amount of tables used, exactly the opposite of what Lanyuan has said.
I've tested this for GROMACS 4.0.4 and from 1 to 190 tables. Near 190
tables, it seems that a threshold in performance starts to form, but n
On 19/07/10 23:18, Lanyuan Lu wrote:
From our group's experience, there is a critical point for dramatic
performance drop when one uses two many tables. The possible reason is that
the size of tables exceeds the cache size. However, this only happens when
the number of tables is beyond something
>From our group's experience, there is a critical point for dramatic
performance drop when one uses two many tables. The possible reason is that
the size of tables exceeds the cache size. However, this only happens when
the number of tables is beyond something like 50. The total table size for
the
On 19/07/10 18:32, Da-Wei Li wrote:
I remember the manu states that it won't cost too much compared with
standard potential function form.
Well, I find in the manual exactly the opposite:
"Note that table lookup is significantly slower than computation of the
most simple Lennard-Jones and Coulo
I remember the manu states that it won't cost too much compared with
standard potential function form.
dawei
On Mon, Jul 19, 2010 at 1:22 PM, ms wrote:
> On 19/07/10 17:32, Da-Wei Li wrote:
>>
>> It will be very little from my experience. Remember that the dominate
>> part is the non-bonded forc
On 19/07/10 17:32, Da-Wei Li wrote:
It will be very little from my experience. Remember that the dominate
part is the non-bonded force calculation.
Well, that's exactly what I tabulate.
dawei
On Mon, Jul 19, 2010 at 12:22 PM, ms wrote:
Hi,
Do you know where can I find some information on
It will be very little from my experience. Remember that the dominate
part is the non-bonded force calculation.
dawei
On Mon, Jul 19, 2010 at 12:22 PM, ms wrote:
> Hi,
>
> Do you know where can I find some information on how using tabulated
> potential affects gmx performance, and how? I have to
Hi,
Do you know where can I find some information on how using tabulated
potential affects gmx performance, and how? I have to decide how to
project a custom model but I don't want to calculate dozens of tables
only to find that gmx grinds to a halt.
thanks!
M.
--
gmx-users mailing listg
Hi
I think this is what you need to do:
(1) Ensure that the topol.top and index.ndx files are set up in the manner
described on the wikki.
(2) Put in the mdp file the following:
energygrps = A B C
energygrp_table = A C B B B C
(3) Now create a set of files as follows
table.xvg - contai
Hi Gromacs users,
previously I've posted my situation with a simulation and I'm still confused:
I have 3 groups of different atoms: A, B and C, and tabulated bonding
and non-bonding potentials.
The tabulated bonded potentials are specified in the files:
table_b1.xvg
table_a1.xvg
table_a2.xvg
ta
> Date: Tue, 1 Dec 2009 07:44:51 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Tabulated potentials make newbies crazy
>
> ms wrote:
> > Mark Abraham ha scritto:
> > > Sorry, I was a bit incomplete
ms wrote:
Mark Abraham ha scritto:
> Sorry, I was a bit incomplete last night. Charge groups are the
fundamental unit for neighbour-searching (3.4.2) to construct lists of
charge groups for nonbonded interactions, which determine lists of
atom-atom interactions. However, the nonbonded interacti
Mark Abraham ha scritto:
> Sorry, I was a bit incomplete last night. Charge groups are the
> fundamental unit for neighbour-searching (3.4.2) to construct lists of
> charge groups for nonbonded interactions, which determine lists of
> atom-atom interactions. However, the nonbonded interactions are
ms wrote:
Dear Mark,
First of all, thanks for your patient and thorough reply!
Mark Abraham ha scritto:
Yeah, that's an unfortunate fact of life. The manual can't be organized
so that everybody finds all the information they want in one location
with the detail they need right now. Using tabul
ms wrote:
Sorry to say I can't help with the larger problem, but I'd like to comment on
this:
The problem is that since I have a single molecule now, and the single
molecule must be neutral, so it must be all a single charge group
("Therefore we have to keep groups of atoms with total char
Dear Mark,
First of all, thanks for your patient and thorough reply!
Mark Abraham ha scritto:
> Yeah, that's an unfortunate fact of life. The manual can't be organized
> so that everybody finds all the information they want in one location
> with the detail they need right now. Using tabulated po
ms wrote:
Hi,
I am really having a hard time figuring out how to use tabulated
potentials correctly.
In general, the information on how to use tables is sparse and scattered
in several points of the manual (ch.5, ch.7, ch.6.7...) -I hope to write
a short howto in the wiki once I get this workin
Hi,
I am really having a hard time figuring out how to use tabulated
potentials correctly.
In general, the information on how to use tables is sparse and scattered
in several points of the manual (ch.5, ch.7, ch.6.7...) -I hope to write
a short howto in the wiki once I get this working, but now I
; From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] tabulated potentials and pairs
>
>
> Dear all,
>
> I simulate a protein in water, and use AMBER03 parameters plus a tabulated
> potential for the Coulomb interactions. Next to the table.xvg file tha
Dear all,
I simulate a protein in water, and use AMBER03 parameters plus a tabulated
potential for the Coulomb interactions. Next to the table.xvg file that i
provide,
mdrun seems to require a second file called tablep.xvg, which is supposed to
contain the corrsponding tabulated pair interact
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