[gmx-users] em.gro file doesnt show a reasonable structure in VMD

Dear gmx users, I have perform an energy minimization on my system and the potential per step plot has a normal appearance, but the em.gro file doesn't show a reasonable structure in VMD. Could you tell me why this happened? Regards, Farideh -- Gromacs Users mailing list * Please search the

Re: [gmx-users] em.gro file doesnt show a reasonable structure in VMD

Hi, Thanks for the answer. I have shred the files via dropbox: https://www.dropbox.com/sh/bgcnpwrbvj7ocxg/AAAFKNlpEs5BREDmFPWoUfGma?dl=0 Truly yours, Farideh On Tue, Aug 25, 2015 at 3:21 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Not with that little information. Is the starting

Re: [gmx-users] em.gro file doesnt show a reasonable structure in VMD

Hi, Not with that little information. Is the starting structure reasonable? Upload a screenshot to a file sharing service and show us what you think is unreasonable :-) Mark On Tue, Aug 25, 2015 at 12:16 PM faride badalkhani farideh.kham...@gmail.com wrote: Dear gmx users, I have perform

Re: [gmx-users] em.gro file doesnt show a reasonable structure in VMD

On 8/25/15 7:51 AM, faride badalkhani wrote: Hi, Thanks for the answer. I have shred the files via dropbox: https://www.dropbox.com/sh/bgcnpwrbvj7ocxg/AAAFKNlpEs5BREDmFPWoUfGma?dl=0 You have no bonded interactions defined in your topology, so naturally everything flies apart. -Justin