Re: [gmx-users] Basic Query

priyanka srivastava wrote: Dear Prof. Spoel, Many thanks for your reply. Since the fourier_n* values are associated with the grid sizing, will these values affect my results drastically? do you suggest resubmitting these runs? regards, Pri... check your md.log file to see what was used. yo

Re: [gmx-users] Basic Query

Dear Prof. Spoel, Many thanks for your reply. Since the fourier_n* values are associated with the grid sizing, will these values affect my results drastically? do you suggest resubmitting these runs? regards, Pri... David van der Spoel <[EMAIL PROTECTED]> wrote: priyanka s

Re: [gmx-users] Basic Query

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 c

Re: [gmx-users] Basic Query

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 f

Re: [gmx-users] Basic Query

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 4.9

Re: [gmx-users] Basic Query

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

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? > A

[gmx-users] Basic Query

Hie all, 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 Although while performing analysis it shows that the x and y dimensions are consta