Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-09 Thread Justin Lemkul
On 11/9/13 9:51 PM, Gianluca Interlandi wrote: On Sat, 9 Nov 2013, Gianluca Interlandi wrote: Just to chime in. Here is a that paper might be helpful in understanding the role of cuoffs in the CHARMM force field: AU STEINBACH, PJ BROOKS, BR AF STEINBACH, PJ BROOKS, BR TI NEW SPHERICAL

[gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-09 Thread Gianluca Interlandi
On Sat, 9 Nov 2013, Gianluca Interlandi wrote: Just to chime in. Here is a that paper might be helpful in understanding the role of cuoffs in the CHARMM force field: AU STEINBACH, PJ BROOKS, BR AF STEINBACH, PJ BROOKS, BR TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES IN MACROMOLE

Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-09 Thread Justin Lemkul
On 11/9/13 4:16 PM, rajat desikan wrote: Hi Justin, I take it that both the sets of parameters should produce identical macroscopic quantities. For the GPU, is this a decent .mdp? cutoff-scheme= Verlet vdwtype = switch rlist= 1.2 ;rlistlong = 1.4

[gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-09 Thread rajat desikan
Hi Justin, I take it that both the sets of parameters should produce identical macroscopic quantities. For the GPU, is this a decent .mdp? cutoff-scheme= Verlet vdwtype = switch rlist= 1.2 ;rlistlong = 1.4 NOT USED IN GPU...IS THI

Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-08 Thread Justin Lemkul
On 11/7/13 11:32 PM, Rajat Desikan wrote: Dear All, The setting that I mentioned above are from Klauda et al., for a POPE membrane system. They can be found in charmm_npt.mdp in lipidbook (link below) http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html Is there any reason not to use their

[gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Rajat Desikan
Dear All, The setting that I mentioned above are from Klauda et al., for a POPE membrane system. They can be found in charmm_npt.mdp in lipidbook (link below) http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html Is there any reason not to use their .mdp parameters for a membrane-protein system?

Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Gianluca Interlandi
Hi Mark! I think that this is the paper that you are referring to: dx.doi.org/10.1021/ct900549r Also for your reference, these are the settings that Justin recommended using with CHARMM in gromacs: vdwtype = switch rlist = 1.2 rlistlong = 1.4 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 As y

Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Mark Abraham
Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM switch differs from the GROMACS switch (Justin linked a paper here with the CHARMM switch description a month or so back, but I don't have that link to hand). Mark On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan wrote: > Than

Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread rajat desikan
Thank you, Mark. I think that running it on CPUs is a safer choice at present. On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham wrote: > Hi, > > It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the > original paper's coulomb settings can be taken with a grain of salt for use >

Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Mark Abraham
Hi, It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the original paper's coulomb settings can be taken with a grain of salt for use with PME - others' success in practice should be a guideline here. The good news is that the default GROMACS PME settings are pretty good for a

[gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Rajat Desikan
Dear All, Any suggestions? Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro