[gmx-users] cut-offs

Dear All, I have read the 'implementation of charmm in gromacs' by bjelkmar, JCTC. There they have used following cut-offs coulombtype=PME rcoulomb=1.2 vdwtype=switch rvdw=1.2 rvdw-switch=1.0 If I use the same numbers with rlist=1.2 it is showing warning saying rlist should be at lear 0.1 - 0.3 n

Re: [gmx-users] CUT-OFFs for GROMOS96 43a1...Reg

Kishore wrote: Dear All, I am running MD simulations of an Alcohol Dehydrogenase ( a tetramer) with the bound NADPH in explicit solvent. I am employing GROMOS96 43a1 force field for the simulations. I need a clarification on the CUT-OFFs applicable for this force field. I have seen many peop

[gmx-users] CUT-OFFs for GROMOS96 43a1...Reg

Dear All, I am running MD simulations of an Alcohol Dehydrogenase ( a tetramer) with the bound NADPH in explicit solvent. I am employing GROMOS96 43a1 force field for the simulations. I need a clarification on the CUT-OFFs applicable for this force field. I have seen many people using *rvdw = 1.4*

Re: [gmx-users] Cut-offs using CHARMM27 ff

On Wed, Dec 1, 2010 at 4:30 PM, Hassan Shallal wrote: > Dear Gromacs users, > > I am trying to use CHARMM27 taking the simulation conditions of two recent > articles as guides in optimizing the simulation parameters. *(DOI: > *10.1021/ct900549r > and *DOI:* 10.1021/jp101581h). > > -- Both are u

[gmx-users] Cut-offs using CHARMM27 ff

Dear Gromacs users, I am trying to use CHARMM27 taking the simulation conditions of two recent articles as guides in optimizing the simulation parameters. (DOI: 10.1021/ct900549r and DOI: 10.1021/jp101581h). -- Both are using PME for electrostatics and I am planning to do that too -- Both ha

Re: [gmx-users] Cut-offs in gromacs

Lum Nforbi wrote: Dear all, I did two md simulations of 200 particles each of a lennard-jones fluid. One of them gave me the correct pair distribution function for a lennard-jones fluid (converging to 1) and one did not (converging to zero). I have attached the .mdp files for both sy

Re: [gmx-users] Cut-offs in gromacs

On 23/02/2010 1:53 PM, Lum Nforbi wrote: Dear all, I did two md simulations of 200 particles each of a lennard-jones fluid. One of them gave me the correct pair distribution function for a lennard-jones fluid (converging to 1) and one did not (converging to zero). I have attached the .m

Re: [gmx-users] Cut-offs in gromacs

Lum Nforbi wrote: Dear all, I did two md simulations of 200 particles each of a lennard-jones fluid. One of them gave me the correct pair distribution function for a lennard-jones fluid (converging to 1) and one did not (converging to zero). I have attached the .mdp files for both

[gmx-users] Cut-offs in gromacs

Dear all, I did two md simulations of 200 particles each of a lennard-jones fluid. One of them gave me the correct pair distribution function for a lennard-jones fluid (converging to 1) and one did not (converging to zero). I have attached the .mdp files for both systems below. The barosta

Re: [gmx-users] cut-offs in j. kerrigans drug/enzyme tutorial

merc mertens wrote: hello, looking at the mdp`s in the above named tutorial, one sees that in em, pr, md the rvdw (1.4 nm) is always bigger than the rcoulomb (1.0 nm). given that electrostatic interactions have a longer range than lennard-jones potentials i do not understand this choice. than

[gmx-users] cut-offs in j. kerrigans drug/enzyme tutorial

hello, looking at the mdp`s in the above named tutorial, one sees that in em, pr, md the rvdw (1.4 nm) is always bigger than the rcoulomb (1.0 nm). given that electrostatic interactions have a longer range than lennard-jones potentials i do not understand this choice. thanks for any help. best