Dear gmx-mail experts, Happy 2013!
I have been struggling to send New-Year greetings using a Thunderbird
list with 50+ addresses, and sought help from GMX support. Below is a
nutshell of the exchanges:
===
*Jan 02*: I get the error message 5.5.3. (more than 26 addresses) while
trying to send
On 1/7/13 7:54 AM, Kabir Roy Chowdhury wrote:
Dear gmx-mail experts, Happy 2013!
I have been struggling to send New-Year greetings using a Thunderbird list with
50+ addresses, and sought help from GMX support. Below is a nutshell of the
exchanges:
===
*Jan 02*: I get the error message 5.5.3.
Sorry, Justin - I should have known better. Please remove my message if
possible.
-kabir...@gmx.com
*On 01/07/2013 02:07 PM, Justin Lemkul wrote:*
On 1/7/13 7:54 AM, Kabir Roy Chowdhury wrote:
Dear gmx-mail experts, Happy 2013!
I have been struggling to send New-Year greetings using a
Hi James,
Don't use the OpenMM accelerated mdrun for explicit solvent simulations.
For such runs any modern CPU with 4-8 cores will probably be as fast or
faster than most GPUs.
However, do consider the 4.6 *native* heterogeneous GPU-accelerated code.
This new efficient code can provide 2-4x
Hi Szilárd!
As I understood you correctly gromacs-4.6 have specific algorithm
(independent on openMM?) for gpu-based calculations havent ? If it
true how I should compilate such new gpu-based gromacs? In the
gromacs-4.6-beta-3 folder I've found instructuon for the standart
installation via cmake
Shima Arasteh shima_arasteh2...@yahoo.com wrote:
Dear Peter,
Would you please let me know how much time approximately the system of
protein/popc took to be npt-equilibrated sufficiently, in accordance
with the simulation you have reported in Beyond modeling paper.
In fact, I put the
I'm trying to compile Gromacs with mopac using the instructions in the tutorial
(the compilation of mopac was made with gfortran since f77 gave me error)
./configure --prefix=/home/raul/gromacs_mopac LIBS=-lmopac
LDFLAGS=-L/home/raul/fftw/lib -L/home/raul/lib CPPFLAGS=-DUSE_MOPAC
Dear Justin,
I have been able to temporarily solve my force field parameter problem (at
least test the new parameters). I defined a new Cys residue say CYSA (as
anion) in the rtp file. But how can I prevent the pdb2gmx from adding
hydrogen to the Cysteine residue? Addition of this extra hydrogen
Two clarifications:
1. can utilization of an index file help during topology generation for my
problem?
2. I use -inter for getting prompted for LYS, ARG, ... but CYS is not one of
them.
Cheers,
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org
On 1/7/13 7:36 PM, Payman Pirzadeh wrote:
Two clarifications:
1. can utilization of an index file help during topology generation for my
problem?
No. Reading pdb2gmx -h will tell you this.
2. I use -inter for getting prompted for LYS, ARG, ... but CYS is not one of
them.
CYS should be
On 1/7/13 6:11 PM, Tom wrote:
Dear Gromacs Users
I want to use harmonic type of improper angle potential with opls-aa
The manu seems not clear.
Can anyone give an small example about the format in *rtp file
and ffbond.itp file?
The names of improper_*_*_*_* tell you to what improper the
I got it.
Thanks for your reply.
Sincerely,
Shima
From: Peter Lai p...@uab.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Monday, January 7, 2013 7:02 PM
Subject: Re: [gmx-users] npt
Dear Justin,
Thanks for your suggestions. It all made sense.
But I ran into a strange problem. I checked the mail list, and all I found
was about misspelling the force field name. I copied the whole gromos53a5.ff
directory into my working folder, copied the modified .rtp, .dat and .hdb
files into
Dear GROMACS Specialists,
I have one system consists of many surfactant molecules that they create
several micelles. How should I know that time of simulation is enough or not?
that means where is the enough time for equilibrium of system?
To creation of micelles, the small oligomers are merged
14 matches
Mail list logo
