Custom Search
-- Dr Ian R Gould Reader in Computational Chemical Biology Department of Chemistry Imperial College London Exhibition Road London SW7 2AY E-mail i.gould.imperial.ac.uk http://www3.imperial.ac.uk/people/i.gould Tel +44 (0)207 594 5809 On 14/09/2012 14:39, "Adrian Roitberg" <roitberg.ufl.edu> wrote: >Callum: > >did you get away with it without needing a surface tension term? That >would be awesome ! > >adrian > > >On 9/14/12 9:36 AM, Dickson, Callum wrote: >> Hi, >> >> All of our runs were on GPUs with the amber11 cuda code, generally >>achieving around 30ns/day for a 72 lipid bilayer (the 288 bilayers were >>around 7ns/day). >> >> Best, >> Callum >> ________________________________________ >> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf >>of Albert [mailmd2011.gmail.com] >> Sent: 14 September 2012 14:29 >> To: AMBER Mailing List >> Subject: Re: [AMBER] GAFFLipid Parameters >> >> hello Ian: >> >> thank you for such generous comments. May I ask was it finished with >> CPU or GPU? and How fast is it? >> >> thank you very much >> Albert >> >> On 09/14/2012 03:10 PM, Dickson, Callum wrote: >>> The standard protocol we used for bilayer simulation is in the methods >>>section of both Lula Rosso's paper from 2008 and our recent paper. We >>>did a two stage minimisation, followed by heating in NVT and further >>>equilibration in NPT. I have put input files for a 72DOPC bilayer below >>>(303K). If you are simulating DPPC or POPE then just change the >>>temperatures accordingly. >>> >>> >>> 1) 72_min1.in >>> >>> first stage minimization >>> &cntrl >>> imin = 1, >>> maxcyc = 1000, >>> ncyc = 250, >>> ntb = 1, >>> ntr = 1, >>> cut = 10, >>> / >>> Hold the solute fixed >>> 500.0 >>> RES 1 72 >>> END >>> END >>> >>> 2) 72_min2.in >>> >>> second step of minimization >>> &cntrl >>> imin = 1, >>> maxcyc = 5000, >>> ncyc = 2500, >>> ntb = 1, >>> ntr = 0, >>> cut = 10 >>> / >>> >>> 3) 72_md1nvt.in >>> >>> nvt run >>> &cntrl >>> ig = -1, >>> imin = 0, >>> nstlim = 10000, >>> dt = 0.002, >>> irest = 0, >>> ntx = 1, >>> ntb = 1, >>> ntt = 3, >>> gamma_ln = 1.0, >>> tempi = 0.0, >>> temp0 = 303, >>> ntr = 1, >>> ntc = 2, >>> ntf = 2, >>> cut = 10, >>> ntpr = 100, >>> ntwx = 100, >>> ntwr = 1000 >>> / >>> Keep solute fixed with weak restraints >>> 10.0 >>> RES 1 72 >>> END >>> END >>> >>> 4) 72_md2npt.in >>> >>> npt run >>> &cntrl >>> imin = 0, >>> nstlim = 25000, dt = 0.002, >>> irest = 1, >>> ntx = 7, >>> ntb = 2, >>> ntp = 2, >>> pres0 = 1.0, >>> taup = 0.5, >>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303, >>> ntr = 0, >>> ntc = 2, ntf = 2, >>> cut = 10, >>> ntpr = 100, ntwx = 100, ntwr = 1000 >>> / >>> >>> 5) 72_md3npt.in >>> >>> npt run >>> &cntrl >>> imin = 0, >>> nstlim = 85000, dt = 0.002, >>> irest = 1, >>> ntx = 7, >>> ntb = 2, >>> ntp = 2, >>> pres0 = 1.0, >>> taup = 1.0, >>> ntt = 3, gamma_ln = 1.0, tempi = 303, temp0 = 303, >>> ntr = 0, >>> ntc = 2, ntf = 2, >>> cut = 10, >>> ntpr = 100, ntwx = 100, ntwr = 1000 >>> / >>> >>> 6) 72_npt_50ns_10Acut.in (Example production run of 50ns) >>> >>> npt production run >>> &cntrl >>> imin = 0, >>> nstlim = 25000000, dt = 0.002, >>> irest = 1, >>> ntx = 7, >>> ntb = 2, >>> ntp = 2, >>> pres0 = 1.0, >>> taup = 1.0, >>> ntt = 3, gamma_ln = 1.0, tempi = 303.0, temp0 = 303.0, >>> ntr = 0, >>> ntc = 2, ntf = 2, >>> cut = 10, >>> ntpr = 5000, ntwx = 5000, ntwr = 50000 >>> / >>> >>> >>> Cheers, >>> Callum >>> >>> PhD Student >>> Institute of Chemical Biology >>> Imperial College London >>> >>> ________________________________________ >>> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf >>>of Albert [mailmd2011.gmail.com] >>> Sent: 14 September 2012 13:39 >>> To: AMBER Mailing List >>> Subject: Re: [AMBER] GAFFLipid Parameters >>> >>> that's nice to hear this news. If possible, would you please also >>> release the input file for simulations since nobody else outside Amber >>> developer has any experience for this and there is no documentation >>>yet. >>> >>> best >>> Albert >>> >>> On 09/14/2012 01:21 PM, Gould, Ian R wrote: >>>> Dear All, >>>> >>>> We have just uploaded our GAFFlipid parameters and other associated >>>>files to LipidBook: >>>> >>>> http://lipidbook.bioch.ox.ac.uk/ >>>> >>>> If you use our parameters please remember to cite our paper. >>>> >>>> Callum J. Dickson , Lula Rosso , Robin M. Betz , Ross C. Walker and >>>>Ian R. Gould, GAFFlipid: a General Amber Force Field for the accurate >>>>molecular dynamics simulation of phospholipid, Soft Matter 8 (2012), >>>>9617-9627, doi: >>>>10.1039/C2SM26007G<http://dx.doi.org/10.1039/C2SM26007G> >>>> >>>> They will also be available from the amber parameter database >>>>maintained by Richard Bryce at Manchester in due course. >>>> >>>> Cheers >>>> Ian >>>> >>>> Women love us for our defects. If we have enough of them, they will >>>>forgive us everything, even our intellects. >>>> Oscar Wilde, >>>> -- >>>> Dr Ian R Gould >>>> Reader in Computational Chemical Biology >>>> Department of Chemistry >>>> Imperial College London >>>> Exhibition Road >>>> London >>>> SW7 2AY >>>> E-mail i.gould.imperial.ac.uk >>>> http://www3.imperial.ac.uk/people/i.gould >>>> Tel +44 (0)207 594 5809 >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > >-- > Dr. Adrian E. Roitberg > Professor > Quantum Theory Project, Department of Chemistry > University of Florida > roitberg.ufl.edu > >_______________________________________________ >AMBER mailing list >AMBER.ambermd.org >http://lists.ambermd.org/mailman/listinfo/amber