[gmx-users] Cut off setting

Hi everyone, I want to calculate the LJ potential with different Cut-off for simulation in a reduced unit (LJ unit). For example, the cut-off for LJ potential of A-A, A-B, and B-B is 1.12246 (repulsive), 1.12246, and 2.5 （attractive, respectively; However, it seems that the Cut-off only can

Re: [gmx-users] Cut off problem with protein in water-vacuum-water layers

On 4/19/13 2:25 PM, Nuria Cirauqui Diaz wrote: Hi all, I am trying to run a simulation of a protein in a water-vacuum-water box, which simulates quite well the membrane environment. I did it some years ago in amber, but know I am trying in grommacs and got the following answer when I try to ru

[gmx-users] Cut off problem with protein in water-vacuum-water layers

Hi all, I am trying to run a simulation of a protein in a water-vacuum-water box, which simulates quite well the membrane environment. I did it some years ago in amber, but know I am trying in grommacs and got the following answer when I try to run the fist "mdp" file: ERROR: The cut-off length i

Re: [gmx-users] cut-off g_hbond

O.K thanks Justin Lemkul wrote: > > > On 10/5/12 8:15 AM, Gavin Melaugh wrote: >> Is there any need to use the r2 option the ? >> > > That option is not relevant here. It is undocumented in the current > release, but the help description has been updated for the next release: > > http://redmine.g

Re: [gmx-users] cut-off g_hbond

On 10/5/12 8:15 AM, Gavin Melaugh wrote: Is there any need to use the r2 option the ? That option is not relevant here. It is undocumented in the current release, but the help description has been updated for the next release: http://redmine.gromacs.org/projects/gromacs/repository/revisi

Re: [gmx-users] cut-off g_hbond

Is there any need to use the r2 option the ? Justin Lemkul wrote: > > > On 10/5/12 7:39 AM, Gavin Melaugh wrote: >> Hi Justin >> >> Thanks, that's what I thought. Is there a need to define a >> hydrogen-acceptor distance as well. I read in a few articles that this >> was the case, usually 0.25nm ?

Re: [gmx-users] cut-off g_hbond

On 10/5/12 7:39 AM, Gavin Melaugh wrote: Hi Justin Thanks, that's what I thought. Is there a need to define a hydrogen-acceptor distance as well. I read in a few articles that this was the case, usually 0.25nm ? One can define hydrogen bonds in a number of ways, but a D-A distance of 0.35 n

Re: [gmx-users] cut-off g_hbond

Hi Justin Thanks, that's what I thought. Is there a need to define a hydrogen-acceptor distance as well. I read in a few articles that this was the case, usually 0.25nm ? Cheers Gavin Justin Lemkul wrote: > > > On 10/5/12 7:20 AM, Gavin Melaugh wrote: >> Hi all >> >> I am using g_hbond to calcu

Re: [gmx-users] cut-off g_hbond

On 10/5/12 7:20 AM, Gavin Melaugh wrote: Hi all I am using g_hbond to calculate the number of hydrogen bonds in an alcohol system. I am using the following command: g_hbond -f traj.trr -nonitacc I am slightly confused about the cut off r. Using the above command, is the default cut-off r (0.

[gmx-users] cut-off g_hbond

Hi all I am using g_hbond to calculate the number of hydrogen bonds in an alcohol system. I am using the following command: g_hbond -f traj.trr -nonitacc I am slightly confused about the cut off r. Using the above command, is the default cut-off r (0.35nm) for the donor-acceptor distance or the

[gmx-users] Cut off problem

Dear Gromacs users, I am using GROMACS 3.3.2. I have a problem in setting the cut off of my MD-run. I want to see the interaction between some small atoms keeping them inside a periodic box without adding any solvent; i.e interaction between the atoms in the vacuum. I have a total of 18-25 atoms

Re: [gmx-users] cut-off

nishap.pa...@utoronto.ca wrote: I see what you mean, so say if I am doing RDF, the values beyond 9A would be bogus? To a large extent, probably, but I don't think that I can say that absolutely without context. For example, you've only shown us rvdw, what about rcoulomb? If it is longer

Re: [gmx-users] cut-off

I see what you mean, so say if I am doing RDF, the values beyond 9A would be bogus? Quoting "Justin A. Lemkul" : nishap.pa...@utoronto.ca wrote: Hello, I wanted to know, if say my box is 30A (cubic) and if I set my cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that

Re: [gmx-users] cut-off

nishap.pa...@utoronto.ca wrote: Hello, I wanted to know, if say my box is 30A (cubic) and if I set my cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean, the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm (to get half the box cut-off)? I am a little

[gmx-users] cut-off

Hello, I wanted to know, if say my box is 30A (cubic) and if I set my cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean, the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm (to get half the box cut-off)? I am a little confused about that. Thanks.