Re: [gmx-users] REMD and GBSA

2011-10-17 Thread Mark Abraham
On 18/10/2011 4:58 AM, Ben Reynwar wrote: On Fri, Oct 14, 2011 at 9:11 AM, Mark Abraham wrote: On 14/10/2011 10:12 AM, Ben Reynwar wrote: Hi gromacs list, I'm about to start some REMD simulations using generalized Born solvent on a protein of about 5000 atoms. I have two questions, the first

Re: [gmx-users] REMD and GBSA

2011-10-17 Thread Ben Reynwar
On Fri, Oct 14, 2011 at 9:11 AM, Mark Abraham wrote: > On 14/10/2011 10:12 AM, Ben Reynwar wrote: >> >> Hi gromacs list, >> >> I'm about to start some REMD simulations using generalized Born >> solvent on a protein of about 5000 atoms.  I have two questions, the >> first of which is about gromacs,

Re: [gmx-users] REMD and GBSA

2011-10-14 Thread Mark Abraham
On 14/10/2011 10:12 AM, Ben Reynwar wrote: Hi gromacs list, I'm about to start some REMD simulations using generalized Born solvent on a protein of about 5000 atoms. I have two questions, the first of which is about gromacs, the second more about REMD in general. (1) I'm getting some pretty ug

[gmx-users] REMD and GBSA

2011-10-13 Thread Ben Reynwar
Hi gromacs list, I'm about to start some REMD simulations using generalized Born solvent on a protein of about 5000 atoms. I have two questions, the first of which is about gromacs, the second more about REMD in general. (1) I'm getting some pretty ugly energy drift (300K->500K in 1 ns) for an N