Hi friends ,
I am new to the REMD simulation.
I read some thread from archive but they not clarify by queries that why I
am asking you on forum
I have following Queries:
1. I want to simulate protein by remd at physiological temp ( 310).
So my initial temp of replica shou
On 10/13/12 4:48 AM, Arman Mahboubi Soufiani wrote:
Dear all friends,
When I want to run a short EM to get my structure more stable for further
equilibration and production steps I get the following error as outpu:
*Library file in current dir nor not found justPLA-em.tpr_d1.xvgin default
di
On 10/13/12 9:05 AM, Arman M. Soufiani wrote:
Dear Justin,
I appreciate your direction. I will try to find out, however, could not fix
it yet.
Providing your exact mdrun command, copied and pasted from the terminal, is the
fastest way to get a solution.
-Justin
--
==
Thanks,
I'll do some test to compare the different choices
regards, Facundo
--
View this message in context:
http://gromacs.5086.n6.nabble.com/small-tc-group-tp5001927p5001986.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gr
Dear Justin,
The followings are the two successive commands I used:
*grompp -f justPLA.mdp -c 20LA-2layer-4chains.gro -p t-PLA.top -o
justPLA-em.tpr
mdrun -deffnm justPLa-em*
BR
Arman
On Sat, Oct 13, 2012 at 3:07 PM, Justin Lemkul wrote:
>
>
> On 10/13/12 9:05 AM, Arman M. Soufiani wrote:
>
Hi all,
I am trying to do an umbrella sampling of a fairly extended state of the
protein along end-to-end distance of it. I am using a rectangular box (
elongated along x ) of dimension 20 nm X 8nm X 8 nm. I am doing the simulation
in NVT ensemble. gromacs 4.5.4 is being used.
But, even after
Dear users,
At Rescale (www.rescale.com) we have developed a cloud simulation
platform to run any type of simulation workflow on-demand. We
specifically focus on highly scalable implementations of compute
intensive simulation codes along with applied math tools to set up
designs of experiment or
On 10/13/12 9:49 AM, Arman Mahboubi Soufiani wrote:
Dear Justin,
The followings are the two successive commands I used:
*grompp -f justPLA.mdp -c 20LA-2layer-4chains.gro -p t-PLA.top -o
justPLA-em.tpr
mdrun -deffnm justPLa-em*
These commands would not produce the error posted previously.
On 10/12/12 2:50 PM, tarak karmakar wrote:
Thanks Justin & Chaban.
Even I did the simulation for 3 ns and it worked well.
Now the issue in my case is , while I was not imposing the M-N
constraints, the metal was rattling around (little bit) and the
histidine residues were moving back and fort
On 10/13/12 3:17 PM, Sanku M wrote:
Hi all,
I am trying to do an umbrella sampling of a fairly extended state of the
protein along end-to-end distance of it. I am using a rectangular box (
elongated along x ) of dimension 20 nm X 8nm X 8 nm. I am doing the simulation
in NVT ensemble. grom
Hi All:
I'm trying to set up a small box with only water and ions (no protein) and
run MD simulation. The commands I used to set up my system and running MD are
as follows:
genbox -cs spc216.gro -o water.gro -maxsol 256 -box 2.1 2.1 2.1
pdb2gmx -f water.gro -q water.pdb -n index.
On 10/13/12 10:32 PM, Liu, Hanzhong wrote:
Hi All:
I'm trying to set up a small box with only water and ions (no protein) and
run MD simulation. The commands I used to set up my system and running MD are
as follows:
genbox -cs spc216.gro -o water.gro -maxsol 256 -box 2.1 2.1 2.1
Thanks! Problem solved!!!
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: Saturday, October 13, 2012 10:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] error: group
Dear Gromacs Users,
I have one system consists of: surfactant, solvent and additives. I made one
box with only solvent and one box with only additives and equilibrated them
little separable for better placing into the box, and then made one box with
surfactant and then placed box of solvent and
14 matches
Mail list logo
