Right, I agree, this was the missing link! I will read the paper, but it
looks like you guys pulled it off. Finally we should be able to simulate
lipids without having to break simple laws of physics like everyone else
has been doing.
I gave up on lipid simulations a long time ago after checking that the
results were simply not believable.
adrian
On 9/14/12 9:44 AM, Dickson, Callum wrote:
> Hi Adrian,
>
> There was no surface tension applied, that was essentially the point of this work if you have a look at the paper! The van der Waals parameters of the lipid carbon chains needed correcting to avoid the use of a surface tension.
> We will be incorporating these parameters with lipid11 soon.
>
> Cheers,
> Callum
> ________________________________________
> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Adrian Roitberg [roitberg.ufl.edu]
> Sent: 14 September 2012 14:39
> To: AMBER Mailing List
> Subject: Re: [AMBER] GAFFLipid Parameters
>
> 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
>>>
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>>
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>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
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--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Fri Sep 14 2012 - 07:00:04 PDT
