[gmx-users] How to implement v-rescale thermostat in gromacs-3.3.3

Hi gmx-users, When I came across the 4.0 beta version, I found there was a new thermostat named v-rescale available here. I wonder if it would be easy to incorporate it in the version 3.3.3 as a patch. Note that the 4.0 version is still under development, I prefer to use a revised 3.3.3 version

[gmx-users] Warning message with 3.3.3 but not with 3.3.1

Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t

[gmx-users] Re: infinite molecule problem - Follow up info

= SOL in my system). Thanks for your attention. > Stop COM of the whole system? > > > > 2008/4/6 Bo Zhou <[EMAIL PROTECTED]>: > > > Dear gmx users, > > > > My previous question are: > > > > >I want to simulate the solid/liquid interface, so

[gmx-users] infinite molecule problem - Follow up info

Dear gmx users, My previous question are: >I want to simulate the solid/liquid interface, so I build an infinite inorganic molecule with pbc=full first. After I ran the system > with vaccum (at the top of system) for a few ps, I found the crystal oscillating along the xy plane collectively and fr

[gmx-users] infinite molecule problem

Dear gmx users, I want to simulate the solid/liquid interface, so I build an infinite inorganic molecule with pbc=full first. After I ran the system with vaccum (at the top of system) for a few ps, I found the crystal oscillating along the xy plane collectively and frequently, so there were too mu

[gmx-users] difference between pbc = full and pbc =xy

Dear all, I want to simulate an infinite inorganic surface in gmx 3.3.3 recently. As I know, pbc = full is required for the bonded interaction on the edges. When I check the newly CVS version, a new set named "pbc = xy" is implemented. I wonder if there is something different between the two sets.

[gmx-users] POL3 polarizable water model

Dear Gromacs users, I wonder whether or not the POL3 polarizable water model (Caldwell JW, Kollman PA (1995) J Phys Chem 99: 6208-6219.) can be incorporated in gmx with amber03 force field. Thanks in advance. Best regards ___ gmx-users mailing list

[gmx-users] Can 1-4 interactions be excluded seperately?

Hi all, There are two molecules in my system. One is parameterized with no torsion term in the energy expression (consistent with the OPLS force field), so 1-4 interactions should be excluded. The other one is treated as a normal protein molecule using OPLS force field. I want to include OPLS ff,

[gmx-users] Re: Question about embedding a force field with no torsion term

ns made by the procedure of genning pairs? Thanks very much. >Bo Zhou wrote: >> Hi all, >> >> >> > >Recently I want to embed a force field (/ Chem. Mater.,/ *17* (23), 5658 > >-5669, 2005) in gmx. In the paper, It is said that the force field >

[gmx-users] Question about embedding a force field with no torsion term

Hi all, Recently I want to embed a force field ( Chem. Mater., 17 (23), 5658 -5669, 2005) in gmx. In the paper, It is said that the force field parameters are consistent with GROMACS. The energy expression has a form as follows: E= E(bond) + E(angle) + E(coulomb) + E(vdW) Note

[gmx-users] surface tension calculation in g_energy

Hi all, I use the option "#Surf*SurfTens" in g_engery to calculate the surface tension, but I find that I really do not know how it works after I get some inconsistent results compared with the calculation using the formula "gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz" ( there are two surfaces here an