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
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Sep 14 2012 - 06:30:04 PDT
