[gmx-users] [Fwd: gen_seed GROMACS]

Original Message Subject: gen_seed GROMACS Date: Sun, 3 Sep 2006 19:36:35 -0700 (PDT) From: Fenghui Fan [EMAIL PROTECTED] To: [EMAIL PROTECTED] Will you please give me an explaination on gen_seed? How can we decide its value? How does it influence the final resuts? What is

[gmx-users] invacuo simulation

Dear gmx users, I am working on protein invacuo simulation in different condition like considering different box size (0.7, 0.8, 1.0) and also with and without pressure coupling. When I am looking at the rmsd and gyration results, they are all varying alot for all the simulations. The

[gmx-users] Tip5p with gromos 96, error atom has mass 0

Hi all: I built a topol file for tip5p water accordint to tip5p.itp which is designed for OPLS.But when i used grompp to built a tpr file,three errors came even the system just have one tip5p water. The error is : ERROR 1 [file "topol.top", line 10]: atom OW Res SOL-1 has

Re: [gmx-users] Tip5p with gromos 96, error atom has mass 0

主月 ：） wrote: Hi all: I built a topol file for tip5p water accordint to tip5p.itp which is designed for OPLS.But when i used grompp to built a tpr file, three errors came even the system just have one tip5p water. The error is : ERROR 1 [file topol.top, line 10]: atom OW Res SOL-1 has

[gmx-users] analyses of g_hbond

Hi, has someone written a script for analyses output of g_hbond. I'm searching for a tool which calculates ratio of hbond to analysis time, and also converts atom nr to atom names. I know only some lines in perl, but if someone has done it, some work has been saved. Greetings, Florian --

Re: [gmx-users] amber ff and cpp error message

On Monday 04 September 2006 11:40, Florian Haberl wrote: Hi, i got a strange behaviour of amberff implementation in gromacs (http://folding.stanford.edu/ffamber/): cpp is not running without problems or warnings: is in faq as e.sorin mailed me

Re: [gmx-users] Question about angle constraints

Hi David,I think maybe the virtual site is suitable for NO3-. But how about PF6-? Please see the .itp file for the PF6-, which is wroten by myself.1. Because all the bond-length are constrainted, there is no energy term in the .itp file. Therefore it is not a problem of energy term, I think. 2.

Re: [gmx-users] Question about angle constraints

Qiao Baofu wrote: Hi David, I think maybe the virtual site is suitable for NO3-. But how about PF6-? Please see the .itp file for the PF6-, which is wroten by myself. 1. Because all the bond-length are constrainted, there is no energy term in the .itp file. Therefore it is not a problem of

[gmx-users] AFM pull and ensembles

Hi all,I have two questions about PMF calculations. 1) Which one is more suggested for an AFM pull simulation, an NVT or an NPT ensemble? I am trying both vacuo and solvated runs (with OPLS-AA ff). 2) My second question is about solvation: I found out that pulling action is much smoother in

[gmx-users] RB-dihedral replacing 1-4 interactions

Bond rotations in the carbon tails were modeled with Ryckaert-Bellemans dihedrals and the corresponding 1,4 interactions removed (Lindahl and Edholm, Biophys J., 79, 426-433) When doing a parameter substitution in this way, exactly what 1,4 interactions should be removed? I am using the pope.itp