[gmx-users] afm pull rate and pull info conflict

Dear Users, While doing the afm pulling I have observed a difference in the units of pull rate between the pull.ppa (nm/ps) and PULL INFO (nm/ns) given in the log output of the run. I am using Gromacs 3.3. Is it a typo error or real ? Attached below is a section of my log file; ***

[gmx-users] How to avoid centering of solute by genbox

Dear gmx users, I am trying to solvate a protein in a rectangular box, keeping it towards one face. But whatever position I choose ( with editconf - translate ), genbox is centering it while solvation. How to override this and keep the protein not at center of box? Thanks in advance. M.N

[gmx-users] Re: gmx-users Digest, Vol 38, Issue 14

er protein. It seems not an issue with the program, but with the protein. U can try running again after a short geometry optimization of the protein (eg: minimization with Argus lab tool). This usually happens for proteins with bad Ramachandran plots. See that also. Good luck. -- M.N.

[gmx-users] Re: error during the minimization

thanks Gurpreet IIT MADRAS -- M.N. MANOJ PROJECT LEADER - BIOINFORMATICS VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION BANGALORE INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Re: error during the minimization

oj I tried the same simulation by taking a structure which was already minimized by another software Amber. Using that structure as the starting structure also, i got the same error i mention earlier. please suggest me something thanks -- M.N. MANOJ PROJECT LEADER - BIOINFORMATICS VITTAL MALLYA SCIENT

[gmx-users] Gromacs scaling problem

comes down with higher job distribution? Kindly advice whats going wrong... Thanks in advance... M.N. Manoj CEO Jigsaw Bio Solutions, Bangalore - INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-us