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[gmx-users] Virtual Sites

I am trying to add virtual sites to a simulation with no mass or charge, just to make tracking the center of mass of groups later easier later on. However, I keep getting the warning The mass of a vsiten constructing atom is = 0 when i run grompp. Here's the section of my .itp file where i

Re: [gmx-users] using nopbc is not equal to using pbc with big box dimensions

Hi, We could guess, or maybe you could share what was in your two .mdp files and how they differ ;-) E.g. report the diff here and upload the originals to an online file-sharing service and link them. Mark On Mon, Dec 2, 2013 at 11:46 PM, Golshan Hejazi golshan.hej...@yahoo.comwrote: Hello,

Re: [gmx-users] Invalid order for directive implicit_genborn_params

Thanks very much Justin, it is working now. -- View this message in context: http://gromacs.5086.x6.nabble.com/Invalid-order-for-directive-implicit-genborn-params-tp5012968p5012978.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please

Re: [gmx-users] using nopbc is not equal to using pbc with big box dimensions

The fact that images are separated by a distance exceeding the cutoff, does not mean that they do not interact electrostatically. I hope the results are not much different... Dr. Vitaly V. Chaban On Mon, Dec 2, 2013 at 11:46 PM, Golshan Hejazi golshan.hej...@yahoo.comwrote: Hello, I