On Sat, Feb 4, 2012 at 8:27 AM, Banafsheh Mehrazma bmehra...@gmail.comwrote:
Dear Justin;
I specified the terminal residues in the *.mdp file, just like what in
my force field has (DNA.rtp) mentioned. I wonder if we should some
thing else with it? I mean, when I viewed my molecule with VMD,
Dear Specialist Gromacs,
I want to compare properties of two micelles of different surfactants by
MARTINI coarse-grained force field.
The difference of these surfactants is in their counterion, one of them has
bromide (Br-) ion and another has Chloride (Cl-). I know that I should show
this
Hi,
The problem might caused by X58 chipset.
Now I am using ubuntu. Which operating system do you recommend?
2012/2/4 David van der Spoel sp...@xray.bmc.uu.se
On 2012-02-03 23:49, ahmet yıldırım wrote:
Dear Mark,
Believe me, I tried all methods that you said but unfortunately the
result
Dear friends,
iam running protein-ligand dynamics.i got an error showing like this
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1228
Fatal error:
moleculetype CU1 is redefined
For more information and tips for troubleshooting, please check the GROMACS
website at
RAMYA NAGA wrote:
Dear friends,
iam running protein-ligand dynamics.i got an error showing like this
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1228
Fatal error:
moleculetype CU1 is redefined
For more information and tips for troubleshooting, please check the GROMACS
thanks for the reply
On Sat, Feb 4, 2012 at 6:36 PM, Justin A. Lemkul jalem...@vt.edu wrote:
RAMYA NAGA wrote:
Dear friends,
iam running protein-ligand dynamics.i got an error showing like this
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1228
Fatal error:
Hey there,
I use it on Ubuntu with no problems whatsoever, but I have Xeon W series CPUs.
GROMACS runs fine with and without HT, so I would also think your problem is
related to your hardware.
Micha
On 4 Feb 2012, at 12:16, ahmet yıldırım
ahmedo...@gmail.commailto:ahmedo...@gmail.com wrote:
On 4/02/2012 11:15 PM, ahmet y?ld?r?m wrote:
Hi,
The problem might caused by X58 chipset.
Now I am using ubuntu. Which operating system do you recommend?
I doubt it is relevant at all.
Mark
2012/2/4 David van der Spoel sp...@xray.bmc.uu.se
mailto:sp...@xray.bmc.uu.se
On 2012-02-03
Dear Gromacs Users!
I have problems during npt equilibration of my solvent box with the CCl4
solvent (I'm preparing this hydrophobic layer for further
membrane-mimicking system).
As the result I want to obtain density value ~ 1.5 for such box but between
2 and 3 ns ( where the desity was 1.3)
James Starlight wrote:
Dear Gromacs Users!
I have problems during npt equilibration of my solvent box with the CCl4
solvent (I'm preparing this hydrophobic layer for further
membrane-mimicking system).
As the result I want to obtain density value ~ 1.5 for such box but
between 2 and 3
Dear Gromacs Users!
I'm investigating activation of the GPCRs receptor in the membrane
Because of potentialy long time required for the activation of such
receptors I want to perform some sort of steered MD simulation. For example
I I want to change rotameric dihedrals of some important swith
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