Re: [gmx-users] system explode when running in MD production

2013-04-21 Thread Justin Lemkul
On 4/21/13 8:09 PM, Nur Syafiqah Abdul Ghani wrote: HI guys, I got this problem when I running my protein and metal in mix solvent. First of all,my question is can we use the original file of pdb and dock it with metal and run it by simulation? Maybe. Dealing with metals is tricky and not

[gmx-users] system explode when running in MD production

2013-04-21 Thread Nur Syafiqah Abdul Ghani
HI guys, I got this problem when I running my protein and metal in mix solvent. First of all,my question is can we use the original file of pdb and dock it with metal and run it by simulation? Second question, after the equilibration part where the pressure and temperature is on.The pressure that

Re: [gmx-users] system explode when running in MD production

2013-04-21 Thread Justin Lemkul
On 4/21/13 8:01 PM, Nur Syafiqah Abdul Ghani wrote: HI guys, I got this problem when I running my protein and metal in mix solvent condition. Please see the standard advice: http://www.gromacs.org/Documentation/Terminology/Blowing_Up Without significantly more detail (your preparation pro

[gmx-users] system explode when running in MD production

2013-04-21 Thread Nur Syafiqah Abdul Ghani
HI guys, I got this problem when I running my protein and metal in mix solvent condition. -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative e