[gmx-users] Installation of 4.0.5 on Cray XD1- gmxtest

sure that these diverging errors are actually errors in the test, (especially since I got NO such errors on the MacBook install of the exact same source files.) Thanks very much for your help. Dean -- Dr. Dean Cuebas, Associate Prof of Chemistry deancue...@missouristate.edu, Ph 417-836-8567 FAX 41

[gmx-users] Suggestions for 3D-monitor/glasses for visualizing GROMACS output

and haven't ever used a 3D workstation before, but I would very much any suggestions. Thanks very much for your help! Dean -- Dr. Dean Cuebas, Associate Professor of Chemistry deancue...@missouristate.edu, Ph 417-836-8567 FAX 417-836-5507 Dept. of Chemistry, Missouri State University Spring

[gmx-users] prodrg 4.5beta generated topologies and exclusions

Hello all. Just a quick clarification, please. Reading the original GROMOS53A6 paper, it appears that 2nd neighbor (1-3) interactions are always excluded, and that third neighbor (1-4) non-bonding interactions are used, yet modified in some circumstances. The paper also states that all (1-4) inter

[gmx-users] Topologies and charges for large organic ligands

Is there an algorithm to generating "improved" charge groups? I ask these questions because my ligands are large organics... MW 800 and greater. Thanks for any and all help in this regard. -- Dr. Dean Cuebas, Associate Prof of Chemistry deancue...@smsu.edu, Ph 417-836-8567 FAX 417-836-5507

[gmx-users] K+ ion missing from gromos96ff in ions.itp file

GROMOS96 force fields? Thanks in advance. Dean -- There are two ways to look at life. One is as though nothing is a miracle; the other is as though everything is. -Albert Einstein Dr. Dean Cuebas dac0...@missouristate.edu, Ph 417-836-8567 FAX 417-836-5507 Dept. of Chemistry, Missouri State University

[gmx-users] pre-compiled MacOS 3.3.2 gmx_sumi error

can get some real work done. Thanks for any and all help!! (Sorry again for the rant.) Dean Dr. Dean Cuebas, Associate Professor of Chemistry deancue...@missouristate.edu, Ph 417-836-8567 FAX 417-836-5507 Dept. of Chemistry, Missouri State University Springfield, Missouri 65

[gmx-users] Re: grompp error- Excluding 3 bonded neighbours-Fatal (Dean Cuebas)

>> >> Dean Cuebas wrote: >> Dear users, >> I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex >> >> I¹ve tried to get grompp to work, but I keep getting the following message: >> __

[gmx-users] grompp error- Excluding 3 bonded neighbours-Fatal error

>> It appears because grompp is ³excluding² the bonded neighbors is what¹s making me end up with the different number of coordinates in my coordinate and topology files. Could anyone please make a suggestion how to fix this fatal error? Below is my .mdp