Re: [gmx-users] the broken of the molecules

r problems, which have been discussed on the mailing list before. Mark - Original Message - From: kecy...@sina.com Date: Monday, September 6, 2010 18:43 Subject: [gmx-users] the broken of the molecules To: gmx-users > Hello, I do the energy minimization of the butylene box , but

Re: [gmx-users] the broken of the molecules

Hi, If I guess you correctly, you probably mean that when you look on your results (using VMD) it seems like it broken. If this is the case, you are OK, it might seems so but it is not, if you indeed used PBC. Best, Itamar On 6/09/2010 6:25 PM, kecy...@sina.com wrote: Hello, I do the ener

[gmx-users] the broken of the molecules

 Hello, I do the energy minimization of the butylene box , but some butylene molecules are broken after that. The butylene itp file is produced by PRODRG, as follows:   [ moleculetype ] ; Name nrexcl BUT  3 [ atoms ] ;   nr  type  resnr resid  atom  cgnr   charge mass 1   C