Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Justin Lemkul
On 7/17/13 10:54 AM, Sainitin Donakonda wrote: I started MD very recently dont have much experience you said i would need .tpr file which doesnot use PME ? how can i get that ? By writing a new .mdp file that doesn't use PME. Please refer to previous discussions on this topic. People ask

Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Sainitin Donakonda
I started MD very recently dont have much experience you said i would need .tpr file which doesnot use PME ? how can i get that ? Thanks, Nitin On Wed, Jul 17, 2013 at 4:46 PM, Justin Lemkul wrote: > > > On 7/17/13 10:43 AM, Sainitin Donakonda wrote: > >> Ok..thanks...so i will use -rerun opti

Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Sainitin Donakonda
Ok..thanks...so i will use -rerun option in final production ..step..as follows...actually i ran 20 ns MD simulation so i used extend option to run everything in cluster in correct time #first 10 ns grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_10.tpr mdrun -s MD_10.tpr

Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Justin Lemkul
On 7/17/13 10:43 AM, Sainitin Donakonda wrote: Ok..thanks...so i will use -rerun option in final production ..step..as follows...actually i ran 20 ns MD simulation so i used extend option to run everything in cluster in correct time #first 10 ns grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol

Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Justin Lemkul
On 7/17/13 10:12 AM, Sainitin Donakonda wrote: Usually i collect data after final production run...after this i take .xtc file and analyze it using various gromacs tools .. And there you have it. LIE is just an analysis method like anything else. There is no purpose in my mind in reanalyzi

Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Sainitin Donakonda
Usually i collect data after final production run...after this i take .xtc file and analyze it using various gromacs tools .. thanks, nitin On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul wrote: > > > On 7/17/13 9:21 AM, Sainitin Donakonda wrote: > >> Hi justin, >> >> Thanks for explaination ..

Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Justin Lemkul
On 7/17/13 9:21 AM, Sainitin Donakonda wrote: Hi justin, Thanks for explaination .. i already ran MD for both ligand alone and protein ligand complex.. So now can you please tell me where should use mdrun -rerun option ..i mean at which stage ..should i used in Energy miniminimzation or NVT

Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Sainitin Donakonda
Hi justin, Thanks for explaination .. i already ran MD for both ligand alone and protein ligand complex.. So now can you please tell me where should use mdrun -rerun option ..i mean at which stage ..should i used in Energy miniminimzation or NVT and NPT equilibration or Production run .. Or sho

Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Justin Lemkul
On 7/17/13 8:54 AM, Sainitin Donakonda wrote: Hi , I want to use g_lie for my protein-drug complex to get binding energy ..i read some information that we need take care some issues if we used PME electrostatics.. Indeed i have used PME in my simulation.. Can any body explain which parameter