Can you explain your question in more detail? What do you think is wrong or
is there some output from AMBER that you do not understand? Do you think
something is wrong with your input?
WHAM calculations are not part of AMBER, so any advice given here is
courtesy only. I'd recommend looking at more standard texts on the subject;
my personal favorite is the book by Frenkel and Smit, although many journal
articles are also excellent.
Regards,
Brian
On Mon, Jul 28, 2014 at 9:22 AM, Marta Wisniewska <
marta.d.wisniewska.gmail.com> wrote:
> Dear All,
> After umbralla-sampling MD simulations, collected data was fixed by using
> WHAM. Tehe simulations were done for a linear dimer in water (explicite), I
> got differnt plot, which I suspected of it. It presented an interaction in
> vacuoe (L-J potential). Below I present the input for MD simulations:
>
>
> &cntrl
> ntx = 7,imin = 0,
> nstlim = 500000, dt = 0.002,
> tautp = 1.0, cut = 9.0,
> ntc = 2, ntf = 2 ntb = 1, igb = 0,
> ntwe = 1000, ntwx = 100, ntwprt = 52, ntpr = 1000,
> temp0=298, nmropt=1,
> ntt = 1, ntp = 0, taup = 0.5,
> vlimit=10.0
> &end
> &wt type='END' &end
>
> DISANG=wiezy_4.in
> LISTOUT=POUT
>
>
> Could anyone help me?
>
> Bests,
> Marta
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
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Received on Mon Jul 28 2014 - 07:00:03 PDT
