Re: [gmx-users] high initial temperature with low ref_T

2006-07-11 Thread Mark Abraham
Dongsheng Zhang wrote: Dear Mark, Do you have any idea what's wrong with my simulation? You can find the mdp file and the description how I set up my system at the bottom of this email. If you're trying to do vacuum simulations with infinite cutoffs and no periodicity, then the .mdp looks fi

Re: [gmx-users] high initial temperature with low ref_T

2006-07-07 Thread Dongsheng Zhang
Dear Mark, Do you have any idea what's wrong with my simulation? You can find the mdp file and the description how I set up my system at the bottom of this email. All the best! Dongsheng On Thu, 2006-07-06 at 19:16 -0400, Dongsheng Zhang wrote: > Mark, > Thank you very much for your reply.

RE: [gmx-users] high initial temperature with low ref_T

2006-07-06 Thread Dongsheng Zhang
On Fri, 2006-07-07 at 09:02 +1000, Dallas B. Warren wrote: > > My system exploded very soon after mdrun. So I outputted the > > log file every step. I found the initial temperature is about > > 800 K even though I set ref_T = 300. Why does this happen? > > What temperature did you specify when g

Re: [gmx-users] high initial temperature with low ref_T

2006-07-06 Thread Dongsheng Zhang
Mark, Thank you very much for your reply. On Fri, 2006-07-07 at 08:51 +1000, Mark Abraham wrote: > > Hello, GMX users, > > > > My system exploded very soon after mdrun. So I outputted the log file > > every step. I found the initial temperature is about 800 K even though I > > set ref_T = 300. Wh

RE: [gmx-users] high initial temperature with low ref_T

2006-07-06 Thread Dallas B. Warren
> My system exploded very soon after mdrun. So I outputted the > log file every step. I found the initial temperature is about > 800 K even though I set ref_T = 300. Why does this happen? What temperature did you specify when generating velocities with grompp? Or if this is a continuation from a

Re: [gmx-users] high initial temperature with low ref_T

2006-07-06 Thread Mark Abraham
> Hello, GMX users, > > My system exploded very soon after mdrun. So I outputted the log file > every step. I found the initial temperature is about 800 K even though I > set ref_T = 300. Why does this happen? First please tell us you've done energy minimization and checked the structure and resul

[gmx-users] high initial temperature with low ref_T

2006-07-06 Thread Dongsheng Zhang
Hello, GMX users, My system exploded very soon after mdrun. So I outputted the log file every step. I found the initial temperature is about 800 K even though I set ref_T = 300. Why does this happen? The following is from my mdp file: tau_t= 0.1 0.1 ref_t