Hi,
The iwrap variable only controls how your output coordinates look; it
does not affect any other aspect of the calculation. What you are
likely seeing here is a statistical issue, i.e. your two separate
simulations have not yet converged.
-Dan
On Fri, Sep 1, 2017 at 7:59 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote:
> Dear all,
> Currently I am working on amyloid aggregation.So I take 5 Abeta-16-22 residue peptide to show amyloid aggregation.In this case I have got different result when I am using iwrap=1 or not.My input files are : 4000ps MD NPT simulation
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> iwrap= 1,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> ig =-1,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 2000000, dt = 0.002,
> ntpr = 2000, ntwx = 2000, ntwr = 2000
> /
>
> And Another is :4000ps MD NPT simulation
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> ig =-1,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 2000000, dt = 0.002,
> ntpr = 2000, ntwx = 2000, ntwr = 2000
> /
>
> When I use iwrap=1 from the starting of production run, in secondary structure analysis I don't get any extended Beta sheet .But when I don't use iwrap(after 72 ns I have to use iwrap=1 to run the simulation more) I get extended beta sheet.I have attached my secondary structure analysis.
> Please help me out .
> Thanks and regardsSaikat
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 01 2017 - 05:30:03 PDT
