Re: [gmx-users] Some molecules disconnected into many parts after EM

Yanmei Song wrote: Dear Justin: - Program mdrun_d, VERSION 4.0.4 Source code file: gmx_fft_mkl.c, line: 825 Fatal error: Error executing Intel MKL FFT. --- I really could not find out what is the reason for the error

Re: [gmx-users] Some molecules disconnected into many parts after EM

Dear Justin: - Program mdrun_d, VERSION 4.0.4 Source code file: gmx_fft_mkl.c, line: 825 Fatal error: Error executing Intel MKL FFT. --- I really could not find out what is the reason for the error above. Do you mean som

Re: [gmx-users] Some molecules disconnected into many parts after EM

Dear Justin: Sorry to bother so many times. After EM everything looks fine. However the mdrun died with the error: --- Program mdrun_d, VERSION 4.0.4 Source code file: gmx_fft_mkl.c, line: 825 Fatal error: Error executing Intel MKL FFT. ---

Re: [gmx-users] Some molecules disconnected into many parts after EM

VMD guesses bonds based on distances, so it is not necessarily very smart. I have no idea why increasing the box causes the molecules to be displayed correctly, other than that VMD cannot deal with the periodicity correctly, as I implied before. Causing all of the molecules to be within the u

Re: [gmx-users] Some molecules disconnected into many parts after EM

Dear Justin: Thanks for your message. When I open the gro file using VMD it shows: atom:1950 bonds 1907 residue:43 I was thinking the problem may not come from the artifact of visualization. Since if the gro file is fine it should be like: atom:1950 bonds 1944 residue:6 because I have 6 chain

RE: [gmx-users] Some molecules disconnected into many parts after EM

sers] Some molecules disconnected into many parts after EM Dear users: I set up a 8nm cubic box with 6 long chain molecules. After EM, there is no error message. However I found that in the gro file by visualization, 2 of the chains has been split in many parts, which means many bonds in the

Re: [gmx-users] Some molecules disconnected into many parts after EM

Yanmei Song wrote: Dear users: I set up a 8nm cubic box with 6 long chain molecules. After EM, there is no error message. However I found that in the gro file by visualization, 2 of the chains has been split in many parts, which means many bonds in the molecules disconnected. And also the o

[gmx-users] Some molecules disconnected into many parts after EM

Dear users: I set up a 8nm cubic box with 6 long chain molecules. After EM, there is no error message. However I found that in the gro file by visualization, 2 of the chains has been split in many parts, which means many bonds in the molecules disconnected. And also the other 4 are good. I checked