Re: [gmx-users] Reg:Equilibration

2010-10-05 Thread Anil Mhashal
Yeah... A equilibration can be complish within the ps n we have to make ensure that the there should not be more fluctuation in the potential energy in other words it should be stabilize. On 5 October 2010 17:47, Justin A. Lemkul wrote: > > > Anil Mhashal wrote: > >> Just plot a graph of the pot

Re: [gmx-users] Reg:Equilibration

2010-10-05 Thread Mark Abraham
- Original Message - From: Anil Mhashal Date: Tuesday, October 5, 2010 23:11 Subject: Re: [gmx-users] Reg:Equilibration To: Discussion list for GROMACS users > Just plot a graph of the potential energy with respect to the time and check > the energy fluctuation, it should b

Re: [gmx-users] Reg:Equilibration

2010-10-05 Thread Justin A. Lemkul
Anil Mhashal wrote: Just plot a graph of the potential energy with respect to the time and check the energy fluctuation, it should be less than 10% of the average potential energy then u can say that ur protein is equilibrated. I would think that, for most systems, a fluctuation of 10% is

Re: [gmx-users] Reg:Equilibration

2010-10-05 Thread Anil Mhashal
Just plot a graph of the potential energy with respect to the time and check the energy fluctuation, it should be less than 10% of the average potential energy then u can say that ur protein is equilibrated. On 5 October 2010 17:16, vinothkumar mohanakrishnan wrote: > hi anil > > i get the pote

Re: [gmx-users] Reg:Equilibration

2010-10-05 Thread vinothkumar mohanakrishnan
hi anil i get the potential energy at the end of the mdrun. if i want to calulate the deviation with what i should compare and calculate the deviation.can you be more specific. Regards Vinoth On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal wrote: > To check ur equilibration, just look at the pote

Re: [gmx-users] Reg:Equilibration

2010-10-05 Thread Anil Mhashal
To check ur equilibration, just look at the potential energy and find out the deviation in the energy if the deviation in the energy is within 10% then ur equilibration is successful... On 5 October 2010 14:56, vinothkumar mohanakrishnan wrote: > Hi all > > Suppose say i have a box of decane mol

Re: [gmx-users] Reg:Equilibration

2010-10-05 Thread Justin A. Lemkul
vinothkumar mohanakrishnan wrote: Hi all Suppose say i have a box of decane molecules and i want to equilibrate. say i have all the necessary files to run mdrun. on what basis i say whether my equilibration is successful r not after the mdrun. what properties i should measure to know whethe