Re: [gmx-users] LINCS

Hi Mark, Thanks for the reply. I accidentally had lincs-iter set to 4 initially because I forgot to change it to 1 after minimization. After looking into the issue some more I determined the odd results to be due to a few stray processes running on the node I was performing the calculation on

[gmx-users] LINCS

Hi all, Will someone please explain to me why I am seeing the following... I am running a protein/ lipid system with position restraints on the protein. I run two identical runs except in one I have lincs-iter = 1 and the other I have lincs-iter = 4. With lincs-iter = 1 I observe 26.0 hrs/ns

[gmx-users] Re: g_order in GROMACS 3.3.2 and 3.3.1

Hi, I've just begun attempting to use g_order on a protein/lipid POPC system. There are a couple things different that I do than you are currently doing. 1) Make sure that the .pdb file you are using with g_order is a trajectory file and not merely a structure file. See this page to double ch

[gmx-users] g_order atom distance warning

Hello, Over the last day I've been working with the g_order utility, assessing the order parameters of a protein embedded POPC system. I created an index file for one of the carbon chains of the POPC, it looks as follows: [ POPC_&_C34 ] 342 394 446 498 550 602 654 706 758 810 862 91