Yes, we primarily use ptraj scripts to do the calculations. That web site is a good resource. I'll repost the link:
http://www.stfc.ac.uk/cse/25249.aspx
One of our collaborators actually contacted that author to see if they wanted to include their code in the official releases of ptraj, but I don't know what the response was. It'd be nice to include in Amber.
The ptraj 'vector' command can give you the x and y dimension from which you can calculate the box area.
Ben
On Jun 18, 2012, at 11:16, "Albert" <mailmd2011.gmail.com> wrote:
> hello Benjamin:
>
> thank you for kind comments.
>
>
> On 06/18/2012 06:28 PM, Benjamin D Madej wrote:
>> Hello Albert,
>>
>> 50ns may not be long enough to converge just your POPE bilayer. Are you able to show the area per lipid vs. time for your simulation?
>>
>> The first screenshot qualitatively looks too ordered. But I can't tell with the second and third.
>>
>> Are you actually calculating an order parameter for your acyl tails? It's fairly common to compare this to experimental order parameter values.
>>>>> I would like to. However, I don't know how to do this in Amber. I
> look through the whole Amber 12 and AmberTools 12 user guide and don't
> find any comments on this. If possible, would you please have some
> comment on how to do this ?
>
>
>>
>> Please see my previous comments about the overly ordered saturated acyl chains in Lipid11.
> yes, I saw that days ago
> /
> "/
>
> /The saturated acyl tail order is an issue we have been working on, and we are currently testing new parameters for their effect on the tail order and on the bilayer structural properties. We'd like to avoid the artificial constant surface tension all together with a parameter set that can run MD with the tensionless NPT ensemble./
>
> /"
> /
>
>>
>> It is possible to extract area per lipid using ptraj. There is a command 'vector' that will output the periodic box dimensions.
>>>> I tried to do this by command 'ptraj'
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "AMBER 12.0 integrated" (4/2012)
> -/- Executable is: "ptraj"
> /-\ Running on 1 processor(s)
> \-/ Input the name of an AMBER prmtop, CHARMM PSF or PDB file:
> POPE.prmtop
> Opened file "apo.prmtop" with mode (r)
> Residue labels:
> PA PE OL PA PE OL PA PE OL PA
> PE OL PA PE OL PA PE OL PA PE
> OL PA PE OL PA PE OL PA PE OL
> PA PE OL PA PE OL PA PE OL PA
> PE OL PA PE OL PA PE OL PA PE
> OL PA PE OL PA PE OL PA PE OL
> PA PE OL PA PE OL PA PE OL PA
> PE OL PA PE OL PA PE OL PA PE
> ....
> PTRAJ: Processing input from "STDIN" ...
>
> then it stack there and I don't get any additional dialogue for
> specifying the trajectories.
>
>
>>
>> Also, surely the protein and the relative number of lipids will play a role in your membrane bound protein system.
> This system contains a protein with around 300 aa protein and 128 POPE
> lipids which should be reasonable for general membrane protein simulations.
>
> thanks again for your kind comments.
>
> best
> Albert
>
>
>>
>> Ben
>> Walker Molecular Dynamics Lab
>>
>> On Jun 18, 2012, at 7:10, "Albert"<mailmd2011.gmail.com> wrote:
>>
>>> hello:
>>>
>>> I am using the following parameters for lipid 11 FF POPE study:
>>>
>>> equilibration
>>> &cntrl
>>> imin=0, irest=1, ntx=5,
>>> nstlim=25000000, 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=26,
>>> /
>>>
>>> and I did two test:
>>>
>>> 1. 50ns for pre-equilibrated POPE (40ns under CHARMM36)
>>> 2. 100 ns for protein/POPE (POPE also equilibrated for 40ns under CHARMM36)
>>>
>>> what I found is that for both cases, the POPE are too 'ordered' and it
>>> has some preference for origination. Does any body have any idea what
>>> happen to those lipids.
>>>
>>> here are three screenshot from VMD for above mentions.
>>>
>>> https://dl.dropbox.com/u/56271062/f/1.jpg
>>> https://dl.dropbox.com/u/56271062/f/2a.jpg
>>> https://dl.dropbox.com/u/56271062/f/2b.jpg
>>>
>>>
>>> BTW, does anybody knows how to calculate area/lipids in Amber so that we
>>> know whether our system is reliable or not?
>>>
>>> thank you very much
>>> Albert
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 18 2012 - 11:30:03 PDT
