Re: [gmx-users] the DNA md simulation

2012-02-04 Thread rajendra kumar
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,

[gmx-users] beads in martini

2012-02-04 Thread mohammad agha
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

Re: [gmx-users] overheating problem

2012-02-04 Thread ahmet yıldırım
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

[gmx-users] Reg error in dynamics

2012-02-04 Thread RAMYA NAGA
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

Re: [gmx-users] Reg error in dynamics

2012-02-04 Thread Justin A. Lemkul
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

Re: [gmx-users] Reg error in dynamics

2012-02-04 Thread RAMYA NAGA
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:

Re: [gmx-users] overheating problem

2012-02-04 Thread Kunze, Micha
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:

Re: [gmx-users] overheating problem

2012-02-04 Thread Mark Abraham
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

[gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

2012-02-04 Thread James Starlight
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)

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

2012-02-04 Thread Justin A. Lemkul
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

[gmx-users] Steered MD simulation

2012-02-04 Thread James Starlight
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