On Fri, Jun 13, 2014 at 5:35 PM, Vu Truong <vutruong.lsp.gmail.com> wrote:
> Hi,
>
> Thanks so much for your response. I am a graduate student and really new in
> Amber which has brought me much in trouble so far. I found this e-mail list
> is very helpful to gain more knowledge.
>
I highly suggest working through the tutorials. Those helped me a lot
when I was first learning Amber. It also helps to go through the manual
and look at what the various input variables control. And, of course,
experiment with different options to become more comfortable with both the
software and the different models developed in the field.
>
> I'm sorry for lack of information that may waste your time. Below is my
> input information and the message in the output file. My system consist of
> a CeF3 crystal structure with the water box on top of it. Im using Amber 9
> and the code is sander.mpi one.
>
> Here is the input file:
> md of water drop on cerium fluoride
> &cntrl
> dielc =1.0, scee = 1.2,
> cut =9.0, nsnb =50, ibelly = 1, bellymask = ":TP4"
> ntx = 1, irest = 0, ipol = 0, iwrap = 1,
> ntf = 2, ntc = 2, tol = 0.00000010100,
> ntb = 1, ntp = 0, temp0 = 298.0, tautp = 3.0, taup =
> 2.0,
> nstlim = 1000, nscm =-1, dt = 0.002, maxcyc = 1000, imin = 0, ntmin =
> 2,
> ntpr =1000, ntwx = 1000, ntt = 3, ntr = 0, a4p=0.106677717,
> jfastw = 0, pres0 = 1.0, tempi = 0.0, gamma_ln = 5.0,
> &end
> &ewald
> indmeth=1, diptau=10.1, skinnb=1.0,
> &end
>
This input file has a lot of variables that are unnecessary and should be
omitted. In particular, you should just keep all &ewald variables at their
default values unless you have a good reason not to.
Other variables that seem strange to be specified are scee, nsnb, jfastw,
tautp, etc. (and I have _no_ idea what a4p is and I can't find any
references to it anywhere in either the manual or the source code).
I highly recommend you audit your input file, going through with the manual
and keeping only those variables you think are important for your
calculation.
Also, you should upgrade to the latest version of AmberTools (AmberTools
14) and use the sander executable from there.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 13 2014 - 16:30:02 PDT
