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
>
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Received on Fri Sep 14 2012 - 07:00:03 PDT
