Re: [gmx-users] Basic Query

2007-06-20 Thread Martin Höfling
Am Mittwoch, 20. Juni 2007 schrieb priyanka srivastava: I am currently involved in doing a lipid-peptide simulation under NPAT conditions. The way I have applied NPAT condition is as follows: ref_p = 0 1 compressibility = 0.0 4.5e-5 with semiisotropic?

Re: [gmx-users] Basic Query

2007-06-20 Thread priyanka srivastava
Hie, Many thanks for your reply. Yes I have used semi-isotropic coupling. Another doubt is why only a value of 4.5e-5? I have used PME and have mentioned rcoulomb in the .mdp file too, which as is pointed out by you, has no meaning!! But does this mean that my mdp file is wrong? Because if PME

Re: [gmx-users] Basic Query

2007-06-20 Thread Mark Abraham
priyanka srivastava wrote: I have used PME and have mentioned rcoulomb in the .mdp file too, which as is pointed out by you, has no meaning!! But does this mean that my mdp file is wrong? Because if PME does not use rcoulomb it shud simply ignore the value. As you'd see by reading sections

Re: [gmx-users] Basic Query

2007-06-20 Thread David van der Spoel
priyanka srivastava wrote: Hie, Many thanks for your reply. Yes I have used semi-isotropic coupling. Another doubt is why only a value of 4.5e-5? I have used PME and have mentioned rcoulomb in the .mdp file too, which as is pointed out by you, has no meaning!! But does this mean that my mdp

Re: [gmx-users] Basic Query

2007-06-20 Thread Martin Höfling
Am Mittwoch, 20. Juni 2007 schrieb Mark Abraham: As you'd see by reading sections 4.9 and 7.3.9 of the manual, Martin's statement isn't right. The grid dimensions are controlled by the two parameters he mentioned, but there are plenty of other parameters that influence PME. Oh, I didn't