Hi all,
For the GROMOS force field there's also the automated topology builder
(ATB) from Alpesh Malde and Alan Mark:
http://compbio.biosci.uq.edu.au/atb/
Cheers,
René
=
René Pool
Division of Molecular and Computational Toxicology
Departmen
Hello,
some days ago you had recomended me to use a dodecahedron box and "pull_dim = Y
Y Y" to try to decrease some error bars I was obtaining in my PMF calculations
(trying to calculate the binding energy of two cyclic peptides).
Now, I have run these calaculations, but I have a doubt for the
Rebeca García Fandiño wrote:
Hello,
some days ago you had recomended me to use a dodecahedron box and
"pull_dim = Y Y Y" to try to decrease some error bars I was obtaining
in my PMF calculations (trying to calculate the binding energy of two
cyclic peptides).
Now, I have run these calacula
Hi all
A very quick question. I have an atom-type labelled CH in the atom-types
with a particular charge, and in the atom list I assign some of these
specific atoms with zero charge as below. When I generate 1,4
interactions using gen_pairs =yes, what charge for the CH type does it
use? Does groma
Gavin Melaugh wrote:
Hi all
A very quick question. I have an atom-type labelled CH in the atom-types
with a particular charge, and in the atom list I assign some of these
specific atoms with zero charge as below. When I generate 1,4
interactions using gen_pairs =yes, what charge for the CH typ
Hi Justin
I have checked the tpr file. Now it seems to assign the the two type of
CHs as the same atom type, but at the same time with the specified
charge from the [atoms] directive, as I expected. Concerning 1-4
interactions and gen_pairs =yes, my concern is this; from the pair list
and using ge
Gavin Melaugh wrote:
Hi Justin
I have checked the tpr file. Now it seems to assign the the two type of
CHs as the same atom type, but at the same time with the specified
charge from the [atoms] directive, as I expected. Concerning 1-4
interactions and gen_pairs =yes, my concern is this; from t
Hi Justin
Sorry to labour on this but:
I don't quite understand what you mean when you say that nonbonded pair
interactions are not Coulombic. Surely nonbonded charged atoms interact
with each other, when close enough? (or by Nonbonded pair interactions
do you explcitly mean 1-4,1-5, etc.)
What a
Gavin Melaugh wrote:
Hi Justin
Sorry to labour on this but:
I don't quite understand what you mean when you say that nonbonded pair
interactions are not Coulombic. Surely nonbonded charged atoms interact
with each other, when close enough? (or by Nonbonded pair interactions
do you explcitly m
Hello Everyone!
I'm with problems using g_disre where, after de execution, the answer is
always
"Segmentation fault".
To minimize the problem I changed for a very small system in the tutorial
sub-directory of gromacs VERSION 4.5.4. I'm not using mpi library.
The distance rest
Francisco Gomes Neto wrote:
Hello Everyone!
I'm with problems using g_disre where, after de execution, the answer is
always
"Segmentation fault".
To minimize the problem I changed for a very small system in the tutorial
sub-directory of gromacs VERSION 4.5.4. I'm not using mpi li
Hi,
I am sorry to bring up a several-days-old post, but if you have time, I am
wondering if you can please help me with two concepts related to the pdf
file at http://www.andrew.cmu.edu/user/adeyoung/july27/withnvt.pdf and
Justin's comments on it.
1. For temperature coupling in NVT simulation
Dear GROMACS users,my system is composed of a repulsive surface with chains grafted on it and other free chains above this immobilized system. I am hesitating whether to use dispersion corrections for the pressure and energy or not. Without these corrections the repulsion of the grafting surface in
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Hi,
I was wondering whether in gromacs 4, one can use replica exchange simulation
in combination with umbrella sampling.
Thanks
Sanku--
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Andrew DeYoung wrote:
Hi,
I am sorry to bring up a several-days-old post, but if you have time, I am
wondering if you can please help me with two concepts related to the pdf
file at http://www.andrew.cmu.edu/user/adeyoung/july27/withnvt.pdf and
Justin's comments on it.
1. For temperature
Zuzana Benkova wrote:
Dear GROMACS users,
my system is composed of a repulsive surface with chains grafted on it
and other free chains above this immobilized system. I am hesitating
whether to use dispersion corrections for the pressure and energy or
not. Without these corrections the repul
Sanku M wrote:
Hi,
I was wondering whether in gromacs 4, one can use replica exchange
simulation in combination with umbrella sampling.
In theory, yes. Whether or not it is efficient or stable is perhaps another
matter.
-Justin
--
Justin A. Lemk
Hi, there,
I am doing a very simple case of a ice cubic box.
I would like to use g_energy to investigate the total kinetic energy of the
system and use g_traj to generate the rotational and translational kinetic
energy separately, by -ekr and -ekt flags. However I found that the sum of the
ro
Hello, dear gromacs users,
I am trying to get a hint of appropriate values of "VdW raii" of carbons.
For this I calculated r_m from gromos53a6. It uses LJ combination rule
#1, so to my understanding the ratio of the last two columns in
ffnonbonded.itp equals sigma^6. From r_m^6 = 2*sigma^6 I could
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