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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--
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
