Re: [gmx-users] Steered Molecular dynamics

bharat gupta wrote: Hi, I want to know is there any well documented tutorial for SMD in gromacs ?? Have you checked the "Tutorials" page on the Gromacs site? http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling If you're wondering about tutorials, that's the plac

[gmx-users] Steered Molecular dynamics

Hi, I want to know is there any well documented tutorial for SMD in gromacs ?? -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51

Re: [gmx-users] Steered molecular dynamics and Parinello-Rahman and bond constraints.

quantrum75 wrote: Hi GMX-users, I am beginning to use the steered molecular dynamics method to perform a potential of mean field calculation. In your experience, does it matter what kind of a thermostat and pressure coupling is used? Does Nose-Hoover and Parinello-Rahman perform better than

[gmx-users] Steered molecular dynamics and Parinello-Rahman and bond constraints.

Hi GMX-users, I am beginning to use the steered molecular dynamics method to perform a potential of mean field calculation. In your experience, does it matter what kind of a thermostat and pressure coupling is used? Does Nose-Hoover and Parinello-Rahman perform better than Berendsen for this pur

[gmx-users] Steered Molecular Dynamics (SMD)

Dear all: These days, I am trying to pull a slab of griphene moving along the Z direction at a constant speed. The slab of griphene contains 700 atoms. After several times of E-mail communication with the Gromacs users, the simulation can run. However, the run didn't produce the results which I

Re: [gmx-users] Steered Molecular Dynamics (SMD) in Gromcas-4.0.5

Hi, you should set one pull group, not 700. The number of atoms in your pull group is 700. Freezing the pull group in x and y direction probably does what you want. Please also consider to upgrade to 4.0.7, which is the most recent stable version. Best, Carsten On Jan 22, 2010, at 7:41 AM, to

[gmx-users] Steered Molecular Dynamics (SMD) in Gromcas-4.0.5

  Dear all:    I’m using Gromacs-4.0.5 and I want to use the pull code to pull a slab of griphene to move along the Z direction in the simulation (Steered Molecular Dynamics-SMD). The griphene has 700 carbon atoms and the positions of the 700 atoms are expected to be immobile in the X and Y

[gmx-users] Steered Molecular Dynamics in GROMACS

Hello, Can anyone describe the general procedure for SMD in GROMACS? (i.e. how you designate which atoms are to be pulled, in what direction, and by what force). Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.o