Dear User,
I have very basic knowledge of linux and relatively new to gromacs too, I
have Dell workstation (OS Fedora 21 ) with NVIDIA graphics card available ,
Just two weeks before I have compiled gromacs without knowing its
capability of GPU , ( I used option of quick installation guide to
Dear Gromacs users,
I am experiencing a strange behavior using Verlet-cutoff scheme
in combination with a water model with virtual sites.
I am simulating an ice slab with NE6 water model. NE6 water model is
used for simulation of ice and it consists of 3 atom sites and 3 virtual
sites.
On Fri, Apr 24, 2015 at 1:38 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Fri, Apr 24, 2015 at 10:55 AM, HongTham hongtham0...@gmail.com wrote:
Hi all gmx user,
I want to ask if there is the way to specialized the residue index to
assign a disulfide bond between 2 apart Cysteins.
On 4/27/15 9:01 AM, Brett wrote:
Dear Justin,
I have read some of the force fields original paper, but my purpose is to use
MD to settle some biological issues, thus I am afraid I do not have such deep
understanding what explained in the original force field papers.
For Force field 6, here
On 4/27/15 1:29 AM, nao.morish...@takeda.com wrote:
Dear Gromacs Users,
I would appreciate you to give me any comments or hints about the question
below.
What makes the calculation time much longer when I calculate a solvation free
energy using the mdp input1 compared to the mdp input2?
On Mon, 27 Apr 2015 07:43:51 -0400
Justin Lemkul jalem...@vt.edu wrote:
Note that without couple-moltype, you're going to be decoupling the
whole system, which is (1) not what you want for calculating
solvation free energy and (2) extremely slow. There is an inherent
slowdown when running
Dear Justin,
I have read some of the force fields original paper, but my purpose is to use
MD to settle some biological issues, thus I am afraid I do not have such deep
understanding what explained in the original force field papers.
For Force field 6, here I mean AMBER99SB_ILDNprotein. For
On Mon, Apr 27, 2015 at 12:26 PM, Ivan Gladich iglad...@sissa.it wrote:
Dear Gromacs users,
I am experiencing a strange behavior using Verlet-cutoff scheme in
combination with a water model with virtual sites.
I am simulating an ice slab with NE6 water model. NE6 water model is used
On 4/27/15 9:02 AM, Hannes Loeffler wrote:
On Mon, 27 Apr 2015 07:43:51 -0400
Justin Lemkul jalem...@vt.edu wrote:
Note that without couple-moltype, you're going to be decoupling the
whole system, which is (1) not what you want for calculating
solvation free energy and (2) extremely slow.
On 4/26/15 10:17 PM, Brett wrote:
Dear All,
In the on-line Justin tutorial on lysozyme, the several mdp files are for the specific
force field OPLS-AA force field. It specifically mentioned Settings, particularly
nonbonded interaction settings, will be different for other force fields.
Hi Justin and Hannes,
Thank you for the replay.
I apologize for the insufficient information.
Actually, I calculated them with couple-moltype = solute and init-lambda-state
= 1.
The other parameters except for fep-lambdas, the number of core(8) and hardware
were same.
When I look at REAL
On 4/27/15 8:34 PM, nao.morish...@takeda.com wrote:
Hi Justin and Hannes,
Thank you for the replay.
I apologize for the insufficient information.
Actually, I calculated them with couple-moltype = solute and init-lambda-state
= 1.
The other parameters except for fep-lambdas, the number
Dear All,
In the MD mdp file for the old version of on-line tutorials for lysozyme, in
the neighbor search, there is an item rlist, but in the MD mdp file for the
new version of on-line tutorials for lysozyme, in the neighbor search, there is
no item rlist. Will you please tell me why?
In
Dear all,
I am trying to simulate a globular protein predicted by Ab-initio method
using web servers, Robetta and Itasser. I am currently using Gromacs 4.6.5.
A problem has occured during the production md run, when my protein starts
to break into fragments while it remains inside the water box.
On Mon, 27 Apr 2015 09:05:05 -0400
Justin Lemkul jalem...@vt.edu wrote:
On 4/27/15 9:02 AM, Hannes Loeffler wrote:
On Mon, 27 Apr 2015 07:43:51 -0400
Justin Lemkul jalem...@vt.edu wrote:
Note that without couple-moltype, you're going to be decoupling the
whole system, which is (1)
Dear All,
I am a beginner in MD and started with Gromacs. I would like to simulate
the dynamics of a homo-dimeric
protein containing 2 Mn atoms at the active site. I would appreciate any
sorts of help in this regards, e.g.,
please share your experience and/or relevant source in the web/published
16 matches
Mail list logo
