Hi Age:
thank you very much for your kind reply. I will try it these days and I
will update my test when it is done.
On 05/14/2012 09:40 AM, Åge Skjevik wrote:
>
> Hi Albert,
>
> Your gamma_ten value is very high, and I think that is the problem. The gamma_ten
> value specifies the surface tension in dynes/cm/interface, which means that you've
> specified a value of 60 dynes/cm/monolayer (120 dynes/cm for the whole bilayer).
> I'm guessing the bilayer is extended too much in the xy dimension and becomes
> compressed in the z dimension. Try with a much lower gamma_ten. We ran POPE
> at a range of surface tensions and found that gamma_ten=26 (=> 26 dynes/cm/leaflet)
> was the best value. We hope to optimize the force field, so that membrane simulations
> in AMBER eventually can be run in the tensionless NPT ensemble.
>
> Best regards,
>
> Åge Skjevik
>
>
>> Date: Mon, 14 May 2012 08:49:44 +0200
>> From: mailmd2011.gmail.com
>> To: amber.ambermd.org
>> Subject: [AMBER] bi-layer membrane system shrink with NPgamaT
>>
>> Dear:
>>
>> I am testing the latest lipids 11 FF with NPgamaT and I found that
>> my POPE shrinked with NPgamaT. here is one of my NPgamaT input file
>>
>> equilibration
>> &cntrl
>> imin=0, irest=1, ntx=5,
>> nstlim=1000000, dt=0.002,
>> ntc=2, ntf=2,
>> cut=10.0, ntb=2, ntp=3, taup=2.0,
>> ntpr=5000, ntwx=5000, ntwr=50000,
>> ntt=1,
>> iwrap=1,
>> temp0=310.0,
>> csurften=3, ninterface=2, gamma_ten=60,
>> restraintmask=':PE&!.H, 1-311&!.H',
>> restraint_wt=50.0
>> /
>>
>> the harmonic restrain on POPE head and protein was stripped off from
>> 50-->0 gradually over 20 ns (with 12 input file). However, at the end of
>> equiliration, I found that bi-layer lipids shrink ed dramatically: I
>> only saw one layer lipids and the original bi-layer crossed with two
>> each other....
>>
>> Does anybody have any idea for this?
>>
>> thank you very much
>>
>> BEST
>> Albert
>>
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>
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Received on Mon May 14 2012 - 01:00:03 PDT
