Re: [gmx-users] g_lie and ligand only simulation

2013-11-06 Thread Kavyashree M
Thank you.. On Wed, Nov 6, 2013 at 7:39 PM, Justin Lemkul wrote: > > > On 11/6/13 5:47 AM, Kavyashree M wrote: > >> Dear users, >> >> Sorry for repeating the same question. I just wanted to know >> whether is it ok if I have rlist > rcoulomb in ligand-water and >> prot-lig-water rerun md (wi

Re: [gmx-users] g_lie and ligand only simulation

2013-11-06 Thread Justin Lemkul
On 11/6/13 5:47 AM, Kavyashree M wrote: Dear users, Sorry for repeating the same question. I just wanted to know whether is it ok if I have rlist > rcoulomb in ligand-water and prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb in the original simulation using PME? The energi

Re: [gmx-users] g_lie and ligand only simulation

2013-11-06 Thread Kavyashree M
Dear users, Sorry for repeating the same question. I just wanted to know whether is it ok if I have rlist > rcoulomb in ligand-water and prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb in the original simulation using PME? Thank you Regards Kavya On Wed, Nov 6, 2013 at 11

Re: [gmx-users] g_lie and ligand only simulation

2013-11-05 Thread Kavyashree M
Dear users, When the simulation was carried out with PME rcoulomb was set equal to rlist. But when I need to to ligand-water simulation without PME (with RF-0) then it requires rlist greater by 0.1-0.3 than rcoulomb. So if I rerun protein-ligand-water simulation there could be more differences in

Re: [gmx-users] g_lie and ligand only simulation

2013-11-02 Thread Kavyashree M
Ok thank you. I thought it was for protein-ligand-water that needs to be rerun without PME. Thanks Regards Kavya On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul wrote: > > > On 11/2/13 12:14 PM, Kavyashree M wrote: > >> Sir, >> >> Thank you. Should the ligand-water MD be done without PME? >> >>

Re: [gmx-users] g_lie and ligand only simulation

2013-11-02 Thread Justin Lemkul
On 11/2/13 12:14 PM, Kavyashree M wrote: Sir, Thank you. Should the ligand-water MD be done without PME? I already answered this. Please read my previous reply again. -Justin Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul wrote: On 11/2/13 1:22 AM, Kavyash

Re: [gmx-users] g_lie and ligand only simulation

2013-11-02 Thread Kavyashree M
Sir, Thank you. Should the ligand-water MD be done without PME? Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul wrote: > > > On 11/2/13 1:22 AM, Kavyashree M wrote: > >> Dear Users, >> >> Its mentioned in the list that it would be >> wrong to use g_lie on a simulation w

Re: [gmx-users] g_lie and ligand only simulation

2013-11-02 Thread Justin Lemkul
On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done wit

Re: [gmx-users] g_lie and ligand only simulation

2013-11-02 Thread Justin Lemkul
On 11/2/13 1:00 AM, Kavyashree M wrote: Dear Gromacs users, I have a protein-ligand in water simulation (Gmx 4.5.3), for calculating free energy of ligand binding, a separate simulation of ligand in water simulation is required (which I read from the list). The question is the protein-ligand i

[gmx-users] g_lie and ligand only simulation

2013-11-01 Thread Kavyashree M
Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? Thank you Regards kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists

[gmx-users] g_lie and ligand only simulation

2013-11-01 Thread Kavyashree M
Dear Gromacs users, I have a protein-ligand in water simulation (Gmx 4.5.3), for calculating free energy of ligand binding, a separate simulation of ligand in water simulation is required (which I read from the list). The question is the protein-ligand is simulated as a dimeric system so is it nec