[gmx-users] About running Production simulation in GPU with twinrange cut-off

Thank you Justin     To check Performance in GPU i Need to  run simulation  with same parameters for r coulomb =  rvdw   rlist        = 0.9        ; short-range neighborlist cutoff (in nm) rcoulomb    = 1.4        ; short-range electrostatic cutoff (in nm) rvdw        

Re: [gmx-users] About running Production simulation in GPU with twinrange cut-off

On 8/11/13 3:02 AM, vidhya sankar wrote: Thank you Justin To check Performance in GPU i Need to run simulation with same parameters for r coulomb = rvdw rlist= 0.9; short-range neighborlist cutoff (in nm) rcoulomb= 1.4;

[gmx-users] About Running production simualtion in GPU

Thank you Justin for your pervious reply                                                                 As you mailed me When using PME,   the rcoulomb is little bit fiexible and Validationof Modification is necessary .  But How to Validate Such Modification ?  i request you Humbly to give

[gmx-users] Cleaning up trajectory files after crash

I recently had a simulation crash where my .trr and .xtc files extend beyond the last checkpoint time (I'm using 4.6.3). Explicitly something like run_002.trr was written after state.cpt. I was wondering if there was a recommended protocol for truncating run_002.trr such that when I restart from

[gmx-users] hessian calculation with periodic boundary condition

Hi, I am trying to use gromacs to do hessian calculations for some of the structures along a trajectory. Do you know whether the normal mode analysis in  gromacs takes into account the periodic boundary condition when computing the 2nd derivative? Thanks! Best JT -- gmx-users mailing list

Re: [gmx-users] hessian calculation with periodic boundary condition

On 2013-08-11 17:00, John Travers wrote: Hi, I am trying to use gromacs to do hessian calculations for some of the structures along a trajectory. Do you know whether the normal mode analysis in gromacs takes into account the periodic boundary condition when computing the 2nd derivative?

Re: [gmx-users] About Running production simualtion in GPU

On 8/11/13 8:50 AM, vidhya sankar wrote: Thank you Justin for your pervious reply As you mailed me When using PME, the rcoulomb is little bit fiexible and Validationof Modification is necessary . But How to Validate Such

Re: [gmx-users] Cleaning up trajectory files after crash

On 8/11/13 9:16 AM, Joshua Adelman wrote: I recently had a simulation crash where my .trr and .xtc files extend beyond the last checkpoint time (I'm using 4.6.3). Explicitly something like run_002.trr was written after state.cpt. I was wondering if there was a recommended protocol for

Re: [gmx-users] Cleaning up trajectory files after crash

On Aug 11, 2013, at 2:12 PM, Justin Lemkul wrote: On 8/11/13 9:16 AM, Joshua Adelman wrote: I recently had a simulation crash where my .trr and .xtc files extend beyond the last checkpoint time (I'm using 4.6.3). Explicitly something like run_002.trr was written after state.cpt. I was

Re: [gmx-users] Cleaning up trajectory files after crash

On 8/11/13 2:33 PM, Joshua Adelman wrote: On Aug 11, 2013, at 2:12 PM, Justin Lemkul wrote: On 8/11/13 9:16 AM, Joshua Adelman wrote: I recently had a simulation crash where my .trr and .xtc files extend beyond the last checkpoint time (I'm using 4.6.3). Explicitly something like

[gmx-users] Lateral Diffusion of Lipids

Dear users, I want to use g_msd to measure diffusion coefficients of lipid bilayer. But i do not know how to choose the reference atom per lipid for an any type of lipid, such as POPC, DOPC,... Where i can get these references ? Thanks so much for any help ! ~Thu -- gmx-users mailing list

[gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy).

(I am re-posting this since my earlier messages seem to be rejected by the mailing list. Please ignore if you are receiving this multiple times.) Hello Francis, One possible origin of the difference might be the usage of either a counter-ion or a background negative charge to neutralize your