[gmx-users] gromacs-4.5.5 cpmd QM/MM versions

Dear All, I am planning to perform a QM/MM calculation of my protein system. Can anybody suggest me whether gromacs-4.5.5 can be patched with any latest version of CPMD? If not, then please suggest me some combination of the gromacs-cpmd versions. I came across this tutorial, but there, both groma

[gmx-users] Re: Unkwown Keyword HILLS

Does anybody have any idea what's the problem? I use the tutorial example and I don't know why it doesn't work. THX On 08/13/2013 07:19 PM, Albert wrote: Dear: I am trying to run plumed with gromacs plugin. Here is my plumed.dat file which I defined two dihedral angels as cvs: *HILLS HEI

[gmx-users] Yet another question about what force field to use

Hi all, Many questions about how to choose a force field are addressed to this list, sorry if this one was already answered. Some argue that proteins are better modeled with ff99sb-ildn or charmm22* because occur great agreement between NMR experiments and simulations when using these force field

Re: [gmx-users] hessian calculation with periodic boundary condition

Hi, Do you know whether the Hessian in Gromacs is computed analytically or numerically? From the manual (Page 52), it seems it is  computed by finite difference method. Is it the case in Gromacs 4.6.3? Thanks Best JT From: David van der Spoel To: gmx-users@

Re: [gmx-users] VDW switched off in CHARMM tip3p model

You could do that, but it's extra cost for no known benefit. See http://dx.doi.org/10.1021/ct900549r On Tue, Aug 13, 2013 at 7:15 PM, Weilong Zhao wrote: > Hi, > > I noticed that for GROMACS versions of 4.5 of later, the force field for > TIP3P water model in CHARMM27.ff package has a following l

Aw: [gmx-users] Force Field for peptides and proteins

There isn't one it depends on your experiment, and what factors you take into account such as resources, time available or what you wish to observe.  All atom is more realistic, but if time retraints or computer resources are limiting, you may wish a partial atom or hybrid atom system.  In addition

[gmx-users] Unkwown Keyword HILLS

Dear: I am trying to run plumed with gromacs plugin. Here is my plumed.dat file which I defined two dihedral angels as cvs: *HILLS HEIGHT 0.3 W_STRIDE 450 WELLTEMPERED SIMTEMP 310 BIASFACTOR 1.96 TORSION LIST 1 4 65 344 SIGMA 0.12 TORSION LIST 2 46 80 656 SIGMA 0.12 ENDMETA* I am using plum

[gmx-users] VDW switched off in CHARMM tip3p model

Hi, I noticed that for GROMACS versions of 4.5 of later, the force field for TIP3P water model in CHARMM27.ff package has a following line included: The following atom types are NOT part of the CHARMM distribution .. . HWT31 1.0080000.417 A 0.0 0.0 ; TIP3p H It