Hi,
I am a new user of the software, i am interested in using the software to
simulate polymer chain in other to find out the properties(mechanical,
structural and dynamics) of the polymer chain. Is there anybody who can
give me guide line on how to go about it with gromacs.
thanks,
ibrahim
--
Hi Bharat,
In addition to the good comments from Chris, mind that to understand
the molecular nature of experimental observations like yours requires
quite a bit of statistics. With just two cases - wild type and
insertion - there is too much uncertainty to claim that possible
differences you obse
you can clone from http://repo.or.cz/r/gromacs.git if you have problems with
a proxy.
On Mon, Mar 21, 2011 at 10:54 PM, Alif M Latif wrote:
> Dear Gromacs Developers,
>
> Just dropping by to say THANK YOU for v4.5.4, surely is updated version of
> 4.5.3 with all the bugfixes yes?. I'm having p
Dear Gromacs Developers,Just dropping by to say THANK YOU for v4.5.4, surely is updated version of 4.5.3 with all the bugfixes yes?. I'm having problem getting past my university's proxy server to use git. Now hopefully I can continue my research and solve git problems later..Your hard work is gre
On 22/03/2011 1:22 PM, Roland Schulz wrote:
On Mon, Mar 21, 2011 at 9:09 PM, Justin A. Lemkul wrote:
Nancy wrote:
Hi All,
I've used used Gromacs under Linux, and I'm wondering whether it can be
used under Windows 7 and/or Snow Leopard (10.6.6).
Theoretically, Gromacs is compatible with any
On Mon, Mar 21, 2011 at 9:09 PM, Justin A. Lemkul wrote:
>
>
> Nancy wrote:
>>
>> Hi All,
>>
>> I've used used Gromacs under Linux, and I'm wondering whether it can be
>> used under Windows 7 and/or Snow Leopard (10.6.6).
>
> Theoretically, Gromacs is compatible with any environment provided you h
Nancy wrote:
Thanks, I appreciate the clarification. Also, can Gromacs be
accelerated with a laptop nVidia GPU (320M)?
All GPU-related information is here:
http://www.gromacs.org/Downloads/Installation_Instructions/Gromacs_on_GPUs
-Justin
Nancy
On Mon, Mar 21, 2011 at 9:09 PM, Justi
Thanks, I appreciate the clarification. Also, can Gromacs be accelerated
with a laptop nVidia GPU (320M)?
Nancy
On Mon, Mar 21, 2011 at 9:09 PM, Justin A. Lemkul wrote:
>
>
> Nancy wrote:
>
>> Hi All,
>>
>> I've used used Gromacs under Linux, and I'm wondering whether it can be
>> used under
Nancy wrote:
Hi All,
I've used used Gromacs under Linux, and I'm wondering whether it can be
used under Windows 7 and/or Snow Leopard (10.6.6).
Theoretically, Gromacs is compatible with any environment provided you have
proper compilers and libraries, etc. Mac operating systems almost alw
Hi All,
I've used used Gromacs under Linux, and I'm wondering whether it can be used
under Windows 7 and/or Snow Leopard (10.6.6).
Thanks in advance,
Nancy
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://
Dear Bharat:
I hope that this doesn't impede others giving you advice about how to
go about doing what you want to do, but here's my two cents for what
it's worth:
My suggestion is to forget about trying to do that. 3-ns simulations
are not going to give you equilibrium populations of con
Hi,
I simulated a protein (GFP) with one of its loop replaced with a longer loop
. After simulating for some 5 to 10 models with different loop sequences , I
decided to carry out wet-lab experiments for one model on the basis of
simulation result. The analysis of simulation was done in the followi
On 22/03/2011 7:44 AM, SHIVANGI NANGIA wrote:
Hello,
I am new gromacs user.
I am trying to set up a water-methanol system with few hyrdroxide ions.
Since hyrdroxide ion does not already exist in gromacs database, I
defined the following in the .rtp file ( I am using ffG53a6)
[ OH ]
[ atoms
Hello,
I am new gromacs user.
I am trying to set up a water-methanol system with few hyrdroxide ions.
Since hyrdroxide ion does not already exist in gromacs database, I defined the
following in the .rtp file ( I am using ffG53a6)
[ OH ]
[ atoms ]
OWOW-1.41000 0
HW1 H 0.
Plus, with such a small number of atoms there is no need to run on more
than a single CPU. You can even run this one on your workstation for a
significant length of simulation time without any real issue.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmac
Dear Gromacs community,
A new maintenance release of Gromacs is available for download at
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz.
Some notable updates in this release:
* Fixed pdb2gmx picking up force field from local instead of library
directory
* Made pdb2gmx vsite generat
Hello,
I am trying to calculate the non normalized dipole moment autocorrelation
function for water. I am using flexible spc water model
(define=-DFLEX_SPC). I am using gromacs 4.0.7 version.
I run the simulation for 4 ns. I run the following command to calculate
the dipole moment autocorrelati
Hi,
I'm about to simulate a disaccharide in water and have created a
topology/ff-mod based on the 56Acarbo parameters based on gromos 53a6 from
"A reoptimized GROMOS force field for hexopyranose-based carbohydrates
accounting for the relative free energies of ring conformers, anomers,
epimer
Dear users:
I recently came across a system that was composed of tip4p water vapor
droplets separated by vacuum. This system is what you might get if you
did a NVT simulation of water with a box that was 10 times too large
for the number of water molecules.
I was surprised to see that thi
Moeed wrote:
Hello,
I am compressing a single extended PE chain (16 nm in length) in a box
of 20nm in vacuo to get a more realistic shape of the polymer. Although
system is small (only 362 atoms), whatever -np # I choose simulation
runs very slowly. Is that because of the presence of voids
Hello,
I am compressing a single extended PE chain (16 nm in length) in a box of
20nm in vacuo to get a more realistic shape of the polymer. Although system
is small (only 362 atoms), whatever -np # I choose simulation runs very
slowly. Is that because of the presence of voids? Is there a way to
ashutosh srivastava wrote:
Thank You
However what i wanted to ask was about the parameters to be used. So it
would be helpful if someone could guide as to how can i get the
parameters that should be used for 3-sulfinoalanine (CSD).
http://www.gromacs.org/Documentation/How-tos/Parameterizat
Thank You
However what i wanted to ask was about the parameters to be used. So it
would be helpful if someone could guide as to how can i get the parameters
that should be used for 3-sulfinoalanine (CSD).
Ashutosh
On Thu, Mar 17, 2011 at 8:37 PM, Justin A. Lemkul wrote:
>
>
> ashutosh srivast
LinkedIn
Ramachandran Gnanasekaran requested to add you as a connection on
LinkedIn:
--
Chinmay,
I'd like to add you to my professional network on LinkedIn.
- Ramachandran
Accept invitation from Ramachandran Gnanasekaran
http://www.linkedin.c
Alif M Latif wrote:
Dear GROMACS users and developers
I had a problem calculating 1/viscosity from my energy file. It's been
said that the bug have been fixed and the way to get it is through git.
I've successfully cloned the gromacs git repo. But I really did not have
any experien
Dear GROMACS users and developersI had a problem calculating 1/viscosity from my energy file. It's been said that the bug have been fixed and the way to get it is through git. I've successfully cloned the gromacs git repo. But I really did not have any experience using git, so I really need the tu
I was also interested in this, and had posted a message about this. I am
interested, like the OP, in an isolated nucleotide molecule, such as
cytosine or guanidine. Does one have to construct a completely new topology
for this?
On Fri, Mar 18, 2011 at 9:04 PM, wrote:
> I know and I apologize, I
Here are the contents of my input coordinate file.
CRYST10.0000.0000.000 90.00 90.00 90.00 P 1 1
ATOM 1 P G A 4 5.488 -0.842 0.708 1.00 0.00
P
ATOM 2 OP1 G A 4 6.418 0.258 1.047 1.00 0.00
O
ATOM 3 OP2 G A 4 5.367
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