Re: [gmx-users] RDF of water

2013-07-31 Thread Justin Lemkul
On 7/31/13 12:18 PM, George Patargias wrote: Hi Justin Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as the the two groups! So there must be a problem with the choice water-water or SOL-SOL for RDF groups. Indeed there would, because then (with -rdf atom) you're ca

Re: [gmx-users] RDF of water

2013-07-31 Thread George Patargias
Hi Justin Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as the the two groups! So there must be a problem with the choice water-water or SOL-SOL for RDF groups. Many thanks! > > > On 7/31/13 10:49 AM, George Patargias wrote: >> Hello >> >> I am trying to calculate the

Re: [gmx-users] RDF of water

2013-07-31 Thread Justin Lemkul
On 7/31/13 10:49 AM, George Patargias wrote: Hello I am trying to calculate the RDF of water with water for a 10 ns MD of pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default -rdf option (atom). The problem is that the integration of the RDF curve up to the first minimum yie

[gmx-users] RDF of water

2013-07-31 Thread George Patargias
Hello I am trying to calculate the RDF of water with water for a 10 ns MD of pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default -rdf option (atom). The problem is that the integration of the RDF curve up to the first minimum yields a zero value which is obviously not right Do